8WAL
Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS.
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth 0] | SCOP2B Superfamily | RING/U-box like | 8039298 | 3000160 | SCOP2B (2022-06-29) |
M [auth D] | SCOP2B Superfamily | Core histone-like | 8042407 | 3001387 | SCOP2B (2022-06-29) |
TA [auth d] | SCOP2B Superfamily | Core histone-like | 8042407 | 3001387 | SCOP2B (2022-06-29) |
N [auth E] | SCOP2B Superfamily | Taf5 N-terminal domain-like | 8034920 | 3001495 | SCOP2B (2022-06-29) |
UA [auth e] | SCOP2B Superfamily | Taf5 N-terminal domain-like | 8034920 | 3001495 | SCOP2B (2022-06-29) |
O [auth F] | SCOP2B Superfamily | Core histone-like | 8081687 | 3001387 | SCOP2B (2022-06-29) |
VA [auth f] | SCOP2B Superfamily | Core histone-like | 8081687 | 3001387 | SCOP2B (2022-06-29) |
P [auth G] | SCOP2B Superfamily | Rap30/74 heterodimerisation domain-like | 8054049 | 3000142 | SCOP2B (2022-06-29) |
Q [auth H] | SCOP2B Superfamily | Core histone-like | 8053232 | 3001387 | SCOP2B (2022-06-29) |
S [auth J] | SCOP2B Superfamily | Core histone-like | 8053233 | 3001387 | SCOP2B (2022-06-29) |
XA [auth j] | SCOP2B Superfamily | Core histone-like | 8053233 | 3001387 | SCOP2B (2022-06-29) |
B [auth 1] | SCOP2B Superfamily | BSD domain-like | 8039783 | 3001039 | SCOP2B (2022-06-29) |
T [auth L] | SCOP2B Superfamily | Core histone-like | 8042408 | 3001387 | SCOP2B (2022-06-29) |
YA [auth l] | SCOP2B Superfamily | Core histone-like | 8042408 | 3001387 | SCOP2B (2022-06-29) |
U [auth O] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), beta-barrel domain | 8037007 | 3001281 | SCOP2B (2022-06-29) |
U [auth O] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), alpha-helical domain | 8037005 | 3001887 | SCOP2B (2022-06-29) |
V [auth P] | SCOP2B Superfamily | TATA-box binding protein-like | 8036293 | 3000705 | SCOP2B (2022-06-29) |
V [auth P] | SCOP2B Superfamily | TATA-box binding protein-like | 8036295 | 3000705 | SCOP2B (2022-06-29) |
W [auth Q] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), alpha-helical domain | 8037001 | 3001887 | SCOP2B (2022-06-29) |
W [auth Q] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), beta-barrel domain | 8037002 | 3001281 | SCOP2B (2022-06-29) |
X [auth R] | SCOP2B Superfamily | Cyclin-like | 8043882 | 3000768 | SCOP2B (2022-06-29) |
X [auth R] | SCOP2B Superfamily | Cyclin-like | 8043880 | 3000768 | SCOP2B (2022-06-29) |
Y [auth S] | SCOP2B Superfamily | Rap30/74 heterodimerisation domain-like | 8003556 | 3000142 | SCOP2B (2022-06-29) |
Z [auth T] | SCOP2B Superfamily | Rap30/74 heterodimerisation domain-like | 8003550 | 3000142 | SCOP2B (2022-06-29) |
Z [auth T] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8003005 | 3000034 | SCOP2B (2022-06-29) |
AA [auth U] | SCOP2B Superfamily | Zinc beta-ribbon | 8043056 | 3001238 | SCOP2B (2022-06-29) |
BA [auth V] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8003067 | 3000034 | SCOP2B (2022-06-29) |
C [auth 2] | SCOP2B Superfamily | Cysteine-rich domain | 8033482 | 3001452 | SCOP2B (2022-06-29) |
C [auth 2] | SCOP2B Superfamily | vWA-like | 8057086 | 3000832 | SCOP2B (2022-06-29) |
EA [auth c] | SCOP2B Superfamily | Core histone-like | 8086844 | 3001387 | SCOP2B (2022-06-29) |
FA [auth k] | SCOP2B Superfamily | Core histone-like | 8036824 | 3001387 | SCOP2B (2022-06-29) |
GA [auth m] | SCOP2B Superfamily | Core histone-like | 8036818 | 3001387 | SCOP2B (2022-06-29) |
KA [auth r] | SCOP2B Superfamily | HRDC-like | 8106072 | 3000132 | SCOP2B (2022-06-29) |
MA [auth t] | SCOP2B Superfamily | RPB6/omega subunit-like | 8106082 | 3000189 | SCOP2B (2022-06-29) |
D [auth 3] | SCOP2B Superfamily | vWA-like | 8054198 | 3000832 | SCOP2B (2022-06-29) |
RA [auth y] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8080728 | 3001655 | SCOP2B (2022-06-29) |
SA [auth z] | SCOP2B Superfamily | RNA polymerase subunits | 8103068 | 3001823 | SCOP2B (2022-06-29) |
F [auth 5] | SCOP2B Superfamily | TFB5-like | 8034306 | 3000733 | SCOP2B (2022-06-29) |
G [auth 6] | SCOP2B Superfamily | RecA-like P-loop NTPases | 8054245 | 3002019 | SCOP2B (2022-06-29) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth 0] | PF17121 | Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_5) | Zinc finger, C3HC4 type (RING finger) | Domain | |
A [auth 0] | PF06391 | CDK-activating kinase assembly factor MAT1 (MAT1) | CDK-activating kinase assembly factor MAT1 | - | Family |
K [auth A] | PF12157 | Protein of unknown function (DUF3591) (DUF3591) | Protein of unknown function (DUF3591) | - | Family |
N [auth E], UA [auth e] | PF04494 | WD40 associated region in TFIID subunit, NTD2 domain (TFIID_NTD2) | WD40 associated region in TFIID subunit, NTD2 domain | - | Family |
N [auth E], UA [auth e] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
O [auth F], VA [auth f] | PF07571 | TAF6 C-terminal HEAT repeat domain (TAF6_C) | TAF6 C-terminal HEAT repeat domain | - | Repeat |
O [auth F], VA [auth f] | PF02969 | TATA box binding protein associated factor (TAF) (TAF) | TATA box binding protein associated factor (TAF) | TAF proteins adopt a histone-like fold. | Domain |
P [auth G] | PF04658 | TAFII55 protein conserved region (TAFII55_N) | TAFII55 protein conserved region | - | Family |
Q [auth H] | PF07524 | Bromodomain associated (Bromo_TP) | Bromodomain associated | This domain is predicted to bind DNA [1] and is often found associated with Pfam:PF00439 and in transcription factors. It has a histone-like fold. | Domain |
Q [auth H] | PF10406 | Transcription factor TFIID complex subunit 8 C-term (TAF8_C) | Transcription factor TFIID complex subunit 8 C-term | This is the C-terminal, Delta, part of the TAF8 protein [1]. The N-terminal is generally the histone fold domain, Bromo_TP (Pfam:PF07524). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several gener ... | Domain |
S [auth J], XA [auth j] | PF03540 | Transcription initiation factor TFIID 23-30kDa subunit (TAF10) | Transcription initiation factor TFIID 23-30kDa subunit | - | Family |
T [auth L], YA [auth l] | PF03847 | Transcription initiation factor TFIID subunit A (TFIID_20kDa) | Transcription initiation factor TFIID subunit A | Domain | |
U [auth O] | PF02751 | Transcription initiation factor IIA, gamma subunit (TFIIA_gamma_C) | Transcription initiation factor IIA, gamma subunit | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA b ... | Domain |
U [auth O] | PF02268 | Transcription initiation factor IIA, gamma subunit, helical domain (TFIIA_gamma_N) | Transcription initiation factor IIA, gamma subunit, helical domain | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA ... | Domain |
U [auth O] | PF04997 | RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1) | RNA polymerase Rpb1, domain 1 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ... | Domain |
V [auth P] | PF04561 | RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2) | RNA polymerase Rpb2, domain 2 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ... | Domain |
V [auth P] | PF00352 | Transcription factor TFIID (or TATA-binding protein, TBP) (TBP) | Transcription factor TFIID (or TATA-binding protein, TBP) | Domain | |
V [auth P] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
W [auth Q] | PF03153 | Transcription factor IIA, alpha/beta subunit (TFIIA) | Transcription factor IIA, alpha/beta subunit | - | Family |
W [auth Q] | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
W [auth Q] | PF01000 | RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac) | RNA polymerase Rpb3/RpoA insert domain | Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal | Domain |
X [auth R] | PF00382 | Transcription factor TFIIB repeat (TFIIB) | Transcription factor TFIIB repeat | Domain | |
X [auth R] | PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family |
Y [auth S] | PF01191 | RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C) | RNA polymerase Rpb5, C-terminal domain | The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. | Domain |
Y [auth S] | PF03871 | RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N) | RNA polymerase Rpb5, N-terminal domain | Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ... | Domain |
Z [auth T] | PF02270 | TFIIF, beta subunit HTH domain (TFIIF_beta) | TFIIF, beta subunit HTH domain | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which ... | Domain |
Z [auth T] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |
Z [auth T] | PF17683 | TFIIF, beta subunit N-terminus (TFIIF_beta_N) | TFIIF, beta subunit N-terminus | - | Family |
AA [auth U] | PF08271 | TFIIB zinc-binding (Zn_Ribbon_TF) | TFIIB zinc-binding | The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ... | Domain |
AA [auth U] | PF02002 | TFIIE alpha subunit (TFIIE_alpha) | TFIIE alpha subunit | - | Family |
AA [auth U] | PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N) | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ... | Domain |
AA [auth U] | PF00575 | S1 RNA binding domain (S1) | S1 RNA binding domain | The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. | Domain |
BA [auth V] | PF18121 | TFA2 Winged helix domain 2 (TFA2_Winged_2) | TFA2 Winged helix domain 2 | This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase [1]. | Domain |
BA [auth V] | PF03870 | RNA polymerase Rpb8 (RNA_pol_Rpb8) | RNA polymerase Rpb8 | - | Family |
CA [auth X] | PF01194 | RNA polymerases N / 8 kDa subunit (RNA_pol_N) | RNA polymerases N / 8 kDa subunit | Domain | |
C [auth 2] | PF04056 | Ssl1-like (Ssl1) | Ssl1-like | - | Family |
C [auth 2] | PF07975 | TFIIH C1-like domain (C1_4) | TFIIH C1-like domain | The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD ... | Domain |
DA [auth Y] | PF13656 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
D [auth 3] | PF03850 | Transcription factor Tfb4 (Tfb4) | Transcription factor Tfb4 | This family appears to be distantly related to the VWA domain. | Domain |
E [auth 4] | PF03849 | Transcription factor Tfb2 (Tfb2) | Transcription factor Tfb2 | - | Family |
E [auth 4] | PF18307 | Transcription factor Tfb2 (p52) C-terminal domain (Tfb2_C) | Transcription factor Tfb2 (p52) C-terminal domain | This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH arc ... | Domain |
G [auth 6] | PF13625 | Helicase conserved C-terminal domain (Helicase_C_3) | Helicase conserved C-terminal domain | This domain family is found in a wide variety of helicases and helicase-related proteins. | Domain |
G [auth 6] | PF04851 | Type III restriction enzyme, res subunit (ResIII) | Type III restriction enzyme, res subunit | - | Family |
G [auth 6] | PF16203 | ERCC3/RAD25/XPB C-terminal helicase (ERCC3_RAD25_C) | ERCC3/RAD25/XPB C-terminal helicase | This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases [1]. | Domain |
H [auth 7] | PF13307 | Helicase C-terminal domain (Helicase_C_2) | Helicase C-terminal domain | This domain is found at the C-terminus of DEAD-box helicases. | Domain |
H [auth 7] | PF06777 | Helical and beta-bridge domain (HBB) | Helical and beta-bridge domain | HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein ... | Domain |
H [auth 7] | PF06733 | DEAD_2 (DEAD_2) | DEAD_2 | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Pharos: Disease Associations Pharos Homepage Annotation
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
J [auth Z] | ATP | |
J [auth Z] | G2L | Parent Component: G |
I [auth N] | CSX | Parent Component: CYS : AA0451 : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 |
I [auth N] | HYP | Parent Component: PRO : AA0451 , AA0030 : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 4-hydroxy-L-proline MOD:00039 |
I [auth N] | ILX | Parent Component: ILE : AA0451 , AA0030 , AA0449 : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 4-hydroxy-L-proline MOD:00039 , (2S,3R,4R)-4,5-dihydroxyisoleucine MOD:01378 |
I [auth N] | TRX | Parent Component: TRP : AA0451 , AA0030 , AA0449 |