5WYK | pdb_00005wyk

Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth 3C]SCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases 8063662 3000118 SCOP2B (2022-06-29)
B [auth 3B]SCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases 8063662 3000118 SCOP2B (2022-06-29)
H [auth 3H]SCOP2B SuperfamilyL30e-like 8033484 3001739 SCOP2B (2022-06-29)
G [auth 3G]SCOP2B SuperfamilyL30e-like 8033484 3001739 SCOP2B (2022-06-29)
T [auth BC]SCOP2B SuperfamilyUTPB complex component-like 8061270 3002330 SCOP2B (2022-06-29)
W [auth CA]SCOP2B SuperfamilyRNA-binding domain, RBD 8053724 3000110 SCOP2B (2022-06-29)
W [auth CA]SCOP2B SuperfamilyRRP7 C-terminal domain-like 8053722 3002219 SCOP2B (2022-06-29)
X [auth CB]SCOP2B SuperfamilyPAP/Archaeal CCA-adding enzyme C-terminal domain-like 8053729 3001147 SCOP2B (2022-06-29)
X [auth CB]SCOP2B SuperfamilyNucleotidyltransferase-like 8053725 3000129 SCOP2B (2022-06-29)
X [auth CB]SCOP2B SuperfamilyPAP/OAS1 substrate-binding domain-like 8053728 3000941 SCOP2B (2022-06-29)
X [auth CB]SCOP2B SuperfamilyPAP/OAS1 substrate-binding domain-like 8053727 3000941 SCOP2B (2022-06-29)
X [auth CB]SCOP2B SuperfamilyNucleotidyltransferase-like 8053726 3000129 SCOP2B (2022-06-29)
X [auth CB]SCOP2B SuperfamilyPAP/Archaeal CCA-adding enzyme C-terminal domain-like 8053730 3001147 SCOP2B (2022-06-29)
Z [auth E2]SCOP2B Superfamilyalpha/beta knot 8037153 3001122 SCOP2B (2022-06-29)
Y [auth E1]SCOP2B Superfamilyalpha/beta knot 8037153 3001122 SCOP2B (2022-06-29)
JA [auth SC]SCOP2B SuperfamilyRibosomal S3Ae-like 8053211 3002166 SCOP2B (2022-06-29)
KA [auth SF]SCOP2B SuperfamilyAlpha-L RNA-binding motif 8052758 3001473 SCOP2B (2022-06-29)
KA [auth SF]SCOP2B SuperfamilyNucleic acid-binding proteins 8052759 3000135 SCOP2B (2022-06-29)
KA [auth SF]SCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8052760 3000334 SCOP2B (2022-06-29)
LA [auth SG]SCOP2B SuperfamilyRibosomal protein S7 8065993 3000799 SCOP2B (2022-06-29)
PA [auth SM]SCOP2B SuperfamilyNucleic acid-binding proteins 8052738 3000135 SCOP2B (2022-06-29)
PA [auth SM]SCOP2B SuperfamilyRibosomal S17 N-terminal domain-like 8052736 3002138 SCOP2B (2022-06-29)
QA [auth SO]SCOP2B SuperfamilyS15/NS1 RNA-binding domain 8052974 3001284 SCOP2B (2022-06-29)
QA [auth SO]SCOP2B SuperfamilyHomeodomain-like 8052973 3000001 SCOP2B (2022-06-29)
RA [auth SP]SCOP2B SuperfamilyTranslational machinery components 8095805 3000571 SCOP2B (2022-06-29)
TA [auth SX]SCOP2B SuperfamilyRibosomal protein S8 8096922 3000709 SCOP2B (2022-06-29)
XA [auth Sd]SCOP2B SuperfamilyNucleic acid-binding proteins 8063430 3000135 SCOP2B (2022-06-29)
SA [auth SR]SCOP2B SuperfamilyRibosomal protein S5 domain 2-like 8103366 3000100 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth 3C]Oxidored_nitroe5wyk3C1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
B [auth 3B]Oxidored_nitroe5wyk3B1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
E [auth 3E]Oxidored_nitroe5wyk3E1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
F [auth 3F]Oxidored_nitroe5wyk3F1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
H [auth 3H]Oxidored_nitroe5wyk3H1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
G [auth 3G]Oxidored_nitroe5wyk3G1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
N [auth AE]e5wykAE1 A: alpha bundlesX: P-loop domains-likeH: RelE-likeT: RelE-likeF:ECOD (develop294)
Q [auth B1]AARP2CNe5wykB11 A: alpha bundlesX: Spectrin repeat-likeH: Spectrin repeatT: Spectrin repeatF: AARP2CNECOD (develop294)
R [auth BA]ECH_1e5wykBA2 A: alpha bundlesX: P-loop domains-likeH: Immunoglobulin-relatedT: HAD-likeF: ECH_1ECOD (develop294)
R [auth BA]Brixe5wykBA4 A: alpha bundlesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: BrixECOD (develop294)
S [auth BB]Oxidored_nitroe5wykBB2 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
S [auth BB]WD40, Beta-prop_WDR3_2nde5wykBB4 A: alpha bundlesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: WD40, Beta-prop_WDR3_2ndECOD (develop294)
U [auth BD]Oxidored_nitroe5wykBD1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
V [auth BE]Oxidored_nitroe5wykBE1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
W [auth CA]KH_NusA_2nde5wykCA1 A: alpha bundlesX: Spectrin repeat-likeH: Spectrin repeatT: Spectrin repeatF: KH_NusA_2ndECOD (develop294)
X [auth CB]Oxidored_nitroe5wykCB1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
Z [auth E2]Oxidored_nitroe5wykE21 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
Y [auth E1]Oxidored_nitroe5wykE11 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
BA [auth K1]Oxidored_nitroe5wykK11 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
CA [auth MA]Oxidored_nitroe5wykMA1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
DA [auth MB]Oxidored_nitroe5wykMB1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
GA [auth R1]Oxidored_nitroe5wykR11 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
JA [auth SC]Oxidored_nitroe5wykSC1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
KA [auth SF]Oxidored_nitroe5wykSF1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
LA [auth SG]Oxidored_nitroe5wykSG1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
MA [auth SI]Oxidored_nitroe5wykSI1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
NA [auth SJ]Oxidored_nitroe5wykSJ1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
OA [auth SK]Oxidored_nitroe5wykSK1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
PA [auth SM]Oxidored_nitroe5wykSM1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
QA [auth SO]Oxidored_nitroe5wykSO1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
RA [auth SP]Oxidored_nitroe5wykSP1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
TA [auth SX]Oxidored_nitroe5wykSX1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
UA [auth SY]Oxidored_nitroe5wykSY1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
VA [auth SZ]Oxidored_nitroe5wykSZ1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
WA [auth Sc]Oxidored_nitroe5wykSc1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
XA [auth Sd]Oxidored_nitroe5wykSd1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
YA [auth Sf]Oxidored_nitroe5wykSf1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
BB [auth U4]Oxidored_nitroe5wykU41 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
CB [auth U5]Oxidored_nitroe5wykU51 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
SA [auth SR]Oxidored_nitroe5wykSR1 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)
D [auth 3D]AARP2CNe5wyk3D1 A: alpha bundlesX: Spectrin repeat-likeH: Spectrin repeatT: Spectrin repeatF: AARP2CNECOD (develop294)
FA [auth P1]Oxidored_nitroe5wykP11 A: alpha bundlesX: Spectrin repeat-likeH: TIM barrelsT: TIM barrelsF: Oxidored_nitroECOD (develop294)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B [auth 3B],
C [auth 3C]		PF01269Fibrillarin (Fibrillarin)FibrillarinDomain
E [auth 3E]PF08156NOP5NT (NUC127) domain (NOP5NT)NOP5NT (NUC127) domainThis N terminal domain is found in RNA-binding proteins of the NOP5 family [1]. Domain
E [auth 3E]PF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
G [auth 3G],
H [auth 3H]		PF01248Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)Ribosomal protein L7Ae/L30e/S12e/Gadd45 familyThis family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].
Domain
N [auth AE]PF12397U3 small nucleolar RNA-associated protein 10 (U3snoRNP10)U3 small nucleolar RNA-associated protein 10- Family
Q [auth B1]PF08142AARP2CN (NUC121) domain (AARP2CN)AARP2CN (NUC121) domainThis domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU [1]. Domain
Q [auth B1]PF00004ATPase family associated with various cellular activities (AAA) (AAA)ATPase family associated with various cellular activities (AAA)AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2]. Domain
R [auth BA]PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
R [auth BA]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
S [auth BB]PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
S [auth BB]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
T [auth BC]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
T [auth BC]PF08625Utp13 specific WD40 associated domain (Utp13)Utp13 specific WD40 associated domainUtp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable o ...Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end [1].
Domain
U [auth BD]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
V [auth BE]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
W [auth CA]PF17799Rrp7 RRM-like N-terminal domain (RRM_Rrp7)Rrp7 RRM-like N-terminal domainThis domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation [1]. Domain
W [auth CA]PF12923Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain (RRP7)Ribosomal RNA-processing protein 7 (RRP7) C-terminal domainRRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly [1]. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle [1-2]. Domain
X [auth CB]PF03813Nrap protein domain 1 (Nrap)Nrap protein domain 1Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1]. This domain has a nucleotidyltransferase structure.
Domain
X [auth CB]PF17403Nrap protein PAP/OAS-like domain (Nrap_D2)Nrap protein PAP/OAS-like domainMembers of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
X [auth CB]PF17406Nrap protein PAP/OAS1-like domain 5 (Nrap_D5)Nrap protein PAP/OAS1-like domain 5Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
X [auth CB]PF17407Nrap protein domain 6 (Nrap_D6)Nrap protein domain 6Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
X [auth CB]PF17404Nrap protein domain 3 (Nrap_D3)Nrap protein domain 3Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
X [auth CB]PF17405Nrap protein nucleotidyltransferase domain 4 (Nrap_D4)Nrap protein nucleotidyltransferase domain 4Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a ...Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus [1]. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [1].
Domain
Y [auth E1],
Z [auth E2]		PF03587EMG1/NEP1 methyltransferase (EMG1)EMG1/NEP1 methyltransferase- Family
BA [auth K1]PF17903Krr1 KH1 domain (KH_KRR1_1st)Krr1 KH1 domainThis entry represents the first KH domain in the KRR1 protein [1]. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1 [1]. Domain
BA [auth K1]PF21800KRR1 small subunit processome component, second KH domain (KH_KRR1_2nd)KRR1 small subunit processome component, second KH domainThis is the second K homology domain (KH2) found in KRR1 small subunit processome component from the fungus Chaetomium thermophilum and similar eukaryotic sequences. Domain
CA [auth MA]PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
DA [auth MB]PF04427Brix domain (Brix)Brix domainDomain
GA [auth R1]PF05189RNA 3'-terminal phosphate cyclase (RTC), insert domain (RTC_insert)RNA 3'-terminal phosphate cyclase (RTC), insert domainRNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ...RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1].
Domain
GA [auth R1]PF01137RNA 3'-terminal phosphate cyclase (RTC)RNA 3'-terminal phosphate cyclaseRNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ...RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1].
Domain
JA [auth SC]PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
KA [auth SF]PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
KA [auth SF]PF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
KA [auth SF]PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
KA [auth SF]PF00467KOW motif (KOW)KOW motif- Family
LA [auth SG]PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. Domain
MA [auth SI]PF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
NA [auth SJ]PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
OA [auth SK]PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PA [auth SM]PF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
PA [auth SM]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17Domain
QA [auth SO]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15Domain
RA [auth SP]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
TA [auth SX]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8Domain
VA [auth SZ]PF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
BB [auth U4]PF04900Fcf1 (Fcf1)Fcf1Fcf1 is a nucleolar protein involved in pre-rRNA processing [1]. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits [1]. Domain
CB [auth U5]PF00687Ribosomal protein L1p/L10e family (Ribosomal_L1)Ribosomal protein L1p/L10e familyThis family includes prokaryotic L1 and eukaryotic L10. Domain
SA [auth SR]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
D [auth 3D]PF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
FA [auth P1]PF17903Krr1 KH1 domain (KH_KRR1_1st)Krr1 KH1 domainThis entry represents the first KH domain in the KRR1 protein [1]. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1 [1]. Domain
FA [auth P1]PF22891Eukaryotic type KH-domain (KH-domain type I) (KH_PNO1_2nd)Eukaryotic type KH-domain (KH-domain type I)This entry represents the second KH domain found in the PNO1 protein. PNO1 is part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 3A]U3 RNA---
B [auth 3B],
C [auth 3C]		rRNA 2'-O-methyltransferase fibrillarin
E [auth 3E]Nucleolar protein 58
F [auth 3F]Ribosomal RNA-processing protein 9
G [auth 3G],
H [auth 3H]		13 kDa ribonucleoprotein-associated protein
I [auth 5A]5ETS RNA---
J [auth AA]Utp4---
K [auth AB]Utp5---
L [auth AC]Utp8---
M [auth AD]Utp9---
N [auth AE]U3 small nucleolar RNA-associated protein 10
O [auth AF]Utp15---
P [auth AG]Utp17---
Q [auth B1]Ribosome biogenesis protein BMS1
R [auth BA]Periodic tryptophan protein 2
S [auth BB]U3 small nucleolar RNA-associated protein 12
T [auth BC]U3 small nucleolar RNA-associated protein 13
U [auth BD]U3 small nucleolar RNA-associated protein 18-
V [auth BE]U3 small nucleolar RNA-associated protein 21-
W [auth CA]Ribosomal RNA-processing protein 7
X [auth CB]U3 small nucleolar RNA-associated protein 22
Y [auth E1],
Z [auth E2]		Ribosomal RNA small subunit methyltransferase NEP1
AA [auth E4]Enp2---
BA [auth K1]KRR1 small subunit processome component
CA [auth MA]U3 small nucleolar ribonucleoprotein protein IMP3
DA [auth MB]U3 small nucleolar ribonucleoprotein protein IMP4
EA [auth MC]Mpp10,U3 small nucleolar RNA-associated protein MPP10
GA [auth R1]RNA 3'-terminal phosphate cyclase-like protein
HA [auth S1]Sof1---
IA [auth SA]18S ribosomal RNA---
JA [auth SC]40S ribosomal protein S1-A
KA [auth SF]40S ribosomal protein S4-A
LA [auth SG]40S ribosomal protein S5
MA [auth SI]40S ribosomal protein S7-A
NA [auth SJ]40S ribosomal protein S8-A
OA [auth SK]40S ribosomal protein S9-A
PA [auth SM]40S ribosomal protein S11-A
QA [auth SO]40S ribosomal protein S13
RA [auth SP]40S ribosomal protein S14-A
TA [auth SX]40S ribosomal protein S22-A
UA [auth SY]40S ribosomal protein S23-A
VA [auth SZ]40S ribosomal protein S24-A
WA [auth Sc]40S ribosomal protein S27-A
XA [auth Sd]40S ribosomal protein S28-A
YA [auth Sf]40S ribosomal protein S30-A
ZA [auth U1]Utp7---
AB [auth U2]Utp11---
BB [auth U4]rRNA-processing protein FCF1
CB [auth U5]Ribosome biogenesis protein UTP30
DB [auth UA]Helical domain protein---
EB [auth UB]Helical domain protein---
FB [auth UC]Unassigned helices---
SA [auth SR]40S ribosomal protein S16-A
D [auth 3D]Nucleolar protein 56
FA [auth P1]Pre-rRNA-processing protein PNO1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B [auth 3B],
C [auth 3C]		IPR000692rRNA 2'-O-methyltransferase fibrillarin-likeFamily
B [auth 3B],
C [auth 3C]		IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
B [auth 3B],
C [auth 3C]		IPR020813Fibrillarin, conserved siteConserved Site
E [auth 3E]IPR042239Nop, C-terminal domainHomologous Superfamily
E [auth 3E]IPR012974Nucleolar protein 58/56, N-terminalDomain
E [auth 3E]IPR002687Nop domainDomain
E [auth 3E]IPR012976NOSICDomain
E [auth 3E]IPR036070Nop domain superfamilyHomologous Superfamily
E [auth 3E]IPR045056Nucleolar protein Nop56/Nop58Family
F [auth 3F]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
F [auth 3F]IPR039241Ribosomal RNA-processing protein Rrp9-likeFamily
F [auth 3F]IPR001680WD40 repeatRepeat
F [auth 3F]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
G [auth 3G],
H [auth 3H]		IPR002415H/ACA ribonucleoprotein complex, subunit Nhp2-likeFamily
G [auth 3G],
H [auth 3H]		IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
G [auth 3G],
H [auth 3H]		IPR018492Ribosomal protein eL8/Nhp2 familyFamily
G [auth 3G],
H [auth 3H]		IPR050257Large ribosomal subunit protein eL8/uL1-likeFamily
G [auth 3G],
H [auth 3H]		IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
G [auth 3G],
H [auth 3H]		IPR004037Large ribosomal subunit protein eL8-like, conserved siteConserved Site
N [auth AE]IPR016024Armadillo-type foldHomologous Superfamily
N [auth AE]IPR040191U3 small nucleolar RNA-associated protein 10Family
N [auth AE]IPR021133HEAT, type 2Repeat
N [auth AE]IPR056473Utp10/HEAT1, HEAT-repeats domainDomain
N [auth AE]IPR011989Armadillo-like helicalHomologous Superfamily
N [auth AE]IPR022125U3 small nucleolar RNA-associated protein 10, N-terminalDomain
N [auth AE]IPR012954BP28, C-terminal domainDomain
Q [auth B1]IPR007034Ribosome biogenesis protein BMS1/TSR1, C-terminalDomain
Q [auth B1]IPR039761Ribosome biogenesis protein Bms1/Tsr1Family
Q [auth B1]IPR003959ATPase, AAA-type, coreDomain
Q [auth B1]IPR012948AARP2CNDomain
Q [auth B1]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
Q [auth B1]IPR030387Bms1/Tsr1-type G domainDomain
Q [auth B1]IPR037875Ribosome biogenesis protein Bms1, N-terminalDomain
R [auth BA]IPR024977Anaphase-promoting complex subunit 4-like, WD40 domainDomain
R [auth BA]IPR019775WD40 repeat, conserved siteConserved Site
R [auth BA]IPR007148Small-subunit processome, Utp12Domain
R [auth BA]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
R [auth BA]IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
R [auth BA]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
R [auth BA]IPR001680WD40 repeatRepeat
R [auth BA]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
R [auth BA]IPR027145Periodic tryptophan protein 2Family
S [auth BB]IPR019775WD40 repeat, conserved siteConserved Site
S [auth BB]IPR007148Small-subunit processome, Utp12Domain
S [auth BB]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
S [auth BB]IPR051570TBC1 domain family involved in cilium biogenesisFamily
S [auth BB]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
S [auth BB]IPR001680WD40 repeatRepeat
S [auth BB]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
T [auth BC]IPR019775WD40 repeat, conserved siteConserved Site
T [auth BC]IPR013934U3 small nucleolar RNA-associated protein 13, C-terminalDomain
T [auth BC]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
T [auth BC]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
T [auth BC]IPR001680WD40 repeatRepeat
T [auth BC]IPR057644WD repeat-containing protein 75, second beta-propellerDomain
T [auth BC]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
U [auth BD]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
U [auth BD]IPR001680WD40 repeatRepeat
U [auth BD]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
U [auth BD]IPR045161U3 small nucleolar RNA-associated protein 18Family
V [auth BE]IPR019775WD40 repeat, conserved siteConserved Site
V [auth BE]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
V [auth BE]IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
V [auth BE]IPR001680WD40 repeatRepeat
V [auth BE]IPR007319WDR36/Utp21, C-terminal domainDomain
V [auth BE]IPR059157WDR36/Utp21, N-terminal domainDomain
V [auth BE]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
W [auth CA]IPR040446Ribosomal RNA-processing protein 7Family
W [auth CA]IPR040447Rrp7, RRM-like N-terminal domainDomain
W [auth CA]IPR024326Ribosomal RNA-processing protein 7, C-terminal domainDomain
X [auth CB]IPR035367Nrap protein, domain 2Domain
X [auth CB]IPR035368Nrap protein, domain 3Domain
X [auth CB]IPR035370Nrap protein, domain 5Domain
X [auth CB]IPR005554NOL6/Upt22Family
X [auth CB]IPR035369Nrap protein, domain 4Domain
X [auth CB]IPR035082Nrap protein domain 1Domain
X [auth CB]IPR035371Nrap protein, domain 6Domain
Y [auth E1],
Z [auth E2]		IPR029026tRNA (guanine-N1-)-methyltransferase, N-terminalHomologous Superfamily
Y [auth E1],
Z [auth E2]		IPR005304Ribosomal biogenesis, methyltransferase, EMG1/NEP1Family
Y [auth E1],
Z [auth E2]		IPR029028Alpha/beta knot methyltransferasesHomologous Superfamily
BA [auth K1]IPR041174KRR1 small subunit processome component, first KH domainDomain
BA [auth K1]IPR024166Ribosomal RNA assembly KRR1Family
BA [auth K1]IPR004087K Homology domainDomain
BA [auth K1]IPR048550KRR1 small subunit processome component, first KH domain, eukaryotesDomain
BA [auth K1]IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily
BA [auth K1]IPR048548KRR1 small subunit processome component, second KH domainDomain
BA [auth K1]IPR048549KRR1 small subunit processome component, second KH domain, eukaryotesDomain
CA [auth MA]IPR002942RNA-binding S4 domainDomain
CA [auth MA]IPR022801Small ribosomal subunit protein uS4Family
CA [auth MA]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
CA [auth MA]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
DA [auth MB]IPR044281U3 snoRNP protein/Ribosome production factor 1Family
DA [auth MB]IPR007109Brix domainDomain
EA [auth MC]IPR012173U3 small nucleolar ribonucleoprotein complex, subunit Mpp10Family
GA [auth R1]IPR013792RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/betaHomologous Superfamily
GA [auth R1]IPR023797RNA 3'-terminal phosphate cyclase domainDomain
GA [auth R1]IPR000228RNA 3'-terminal phosphate cyclaseFamily
GA [auth R1]IPR020719RNA 3'-terminal phosphate cyclase-like, conserved siteConserved Site
GA [auth R1]IPR037136RNA 3'-terminal phosphate cyclase domain superfamilyHomologous Superfamily
GA [auth R1]IPR016443RNA 3'-terminal phosphate cyclase type 2Family
GA [auth R1]IPR013791RNA 3'-terminal phosphate cyclase, insert domainDomain
GA [auth R1]IPR036553RNA 3'-terminal phosphate cyclase, insert domain superfamilyHomologous Superfamily
JA [auth SC]IPR001593Small ribosomal subunit protein eS1Family
JA [auth SC]IPR018281Small ribosomal subunit protein eS1, conserved siteConserved Site
JA [auth SC]IPR027500Small ribosomal subunit protein eS1, eukaryotaFamily
KA [auth SF]IPR018199Small ribosomal subunit protein eS4, N-terminal, conserved siteConserved Site
KA [auth SF]IPR013843Small ribosomal subunit protein eS4, N-terminalDomain
KA [auth SF]IPR032277Small ribosomal subunit protein eS4, C-terminal domainDomain
KA [auth SF]IPR002942RNA-binding S4 domainDomain
KA [auth SF]IPR013845Small ribosomal subunit protein eS4, central regionDomain
KA [auth SF]IPR000876Small ribosomal subunit protein eS4Family
KA [auth SF]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
KA [auth SF]IPR038237Small ribosomal subunit protein eS4, central domain superfamilyHomologous Superfamily
KA [auth SF]IPR041982Small ribosomal subunit protein eS4, KOW domainDomain
KA [auth SF]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
KA [auth SF]IPR005824KOWDomain
LA [auth SG]IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
LA [auth SG]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
LA [auth SG]IPR000235Small ribosomal subunit protein uS7Family
LA [auth SG]IPR023798Small ribosomal subunit protein uS7 domainDomain
LA [auth SG]IPR005716Ribosomal protein uS7, eukaryotic/archaealFamily
MA [auth SI]IPR000554Small ribosomal subunit protein eS7Family
MA [auth SI]IPR047861Small ribosomal subunit protein eS7, conserved siteConserved Site
NA [auth SJ]IPR001047Small ribosomal subunit protein eS8Family
NA [auth SJ]IPR042563Small ribosomal subunit protein eS8 subdomain, eukaryotaHomologous Superfamily
NA [auth SJ]IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
NA [auth SJ]IPR018283Small ribosomal subunit protein eS8, conserved siteConserved Site
OA [auth SK]IPR002942RNA-binding S4 domainDomain
OA [auth SK]IPR022801Small ribosomal subunit protein uS4Family
OA [auth SK]IPR005710Small ribosomal subunit protein uS4, eukaryota/archaeaFamily
OA [auth SK]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
OA [auth SK]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
OA [auth SK]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
PA [auth SM]IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
PA [auth SM]IPR032440Small ribosomal subunit protein uS17, N-terminalDomain
PA [auth SM]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
PA [auth SM]IPR000266Small ribosomal subunit protein uS17Family
PA [auth SM]IPR028333Small ribosomal subunit protein uS17, archaeal/eukaryoticFamily
QA [auth SO]IPR012606Small ribosomal subunit protein uS15, N-terminalDomain
QA [auth SO]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
QA [auth SO]IPR000589Small ribosomal subunit protein uS15Family
QA [auth SO]IPR023029Small ribosomal subunit protein uS15, archaea/eukaryotaFamily
RA [auth SP]IPR001971Small ribosomal subunit protein uS11Family
RA [auth SP]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
RA [auth SP]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
TA [auth SX]IPR000630Small ribosomal subunit protein uS8Family
TA [auth SX]IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
TA [auth SX]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
UA [auth SY]IPR006032Small ribosomal subunit protein uS12Family
UA [auth SY]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
UA [auth SY]IPR005680Small ribosomal subunit protein uS12, eukaryota/archaeaFamily
VA [auth SZ]IPR053709Eukaryotic Ribosomal Protein eS24Homologous Superfamily
VA [auth SZ]IPR001976Small ribosomal subunit protein eS24Family
VA [auth SZ]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
VA [auth SZ]IPR018098Small ribosomal subunit protein eS24 conserved siteConserved Site
WA [auth Sc]IPR023407Small ribosomal subunit protein eS27, zinc-binding domain superfamilyHomologous Superfamily
WA [auth Sc]IPR000592Small ribosomal subunit protein eS27Family
WA [auth Sc]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
XA [auth Sd]IPR028626Ribosomal protein eS28 conserved siteConserved Site
XA [auth Sd]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
XA [auth Sd]IPR000289Small ribosomal subunit protein eS28Family
YA [auth Sf]IPR006846Small ribosomal subunit protein eS30Family
BB [auth U4]IPR002716PIN domainDomain
BB [auth U4]IPR006984Fcf1/UTP23Family
BB [auth U4]IPR029060PIN-like domain superfamilyHomologous Superfamily
BB [auth U4]IPR037503rRNA-processing protein Fcf1, PIN domainDomain
CB [auth U5]IPR050257Large ribosomal subunit protein eL8/uL1-likeFamily
CB [auth U5]IPR023674Ribosomal protein uL1-likeHomologous Superfamily
CB [auth U5]IPR028364Ribosomal protein uL1/ribosomal biogenesis proteinFamily
SA [auth SR]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
SA [auth SR]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
SA [auth SR]IPR000754Small ribosomal subunit protein uS9Family
SA [auth SR]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
D [auth 3D]IPR042239Nop, C-terminal domainHomologous Superfamily
D [auth 3D]IPR012974Nucleolar protein 58/56, N-terminalDomain
D [auth 3D]IPR002687Nop domainDomain
D [auth 3D]IPR012976NOSICDomain
D [auth 3D]IPR036070Nop domain superfamilyHomologous Superfamily
D [auth 3D]IPR045056Nucleolar protein Nop56/Nop58Family
FA [auth P1]IPR041174KRR1 small subunit processome component, first KH domainDomain
FA [auth P1]IPR055212PNO1, first type I KH domainDomain
FA [auth P1]IPR055211PNO1, second type I KH domainDomain
FA [auth P1]IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily