1I5L

CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1i5la_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
D [auth B]	d1i5lb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
E [auth C]	d1i5lc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
F [auth D]	d1i5ld_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
G [auth E]	d1i5le_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
H [auth F]	d1i5lf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
I [auth G]	d1i5lg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
J [auth H]	d1i5lh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
K [auth I]	d1i5li_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
L [auth J]	d1i5lj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
M [auth K]	d1i5lk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
N [auth L]	d1i5ll_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
O [auth M]	d1i5lm_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
P [auth N]	d1i5ln_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
J [auth H]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
K [auth I]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
M [auth K]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
N [auth L]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
O [auth M]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
P [auth N]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	LSM	e1i5lA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D [auth B]	LSM	e1i5lB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E [auth C]	LSM	e1i5lC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F [auth D]	LSM	e1i5lD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G [auth E]	LSM	e1i5lE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H [auth F]	LSM	e1i5lF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I [auth G]	LSM	e1i5lG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J [auth H]	LSM	e1i5lH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K [auth I]	LSM	e1i5lI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L [auth J]	LSM	e1i5lJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M [auth K]	LSM	e1i5lK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
N [auth L]	LSM	e1i5lL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
O [auth M]	LSM	e1i5lM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
P [auth N]	LSM	e1i5lN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D [auth B]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E [auth C]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F [auth D]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G [auth E]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H [auth F]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I [auth G]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J [auth H]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
K [auth I]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L [auth J]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
M [auth K]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
N [auth L]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
O [auth M]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
P [auth N]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	PF01423	LSM domain (LSM)	LSM domain	The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...	The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth U], B [auth Y]	5'-R(UPUP*U)-3'	-	-	-
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1	RNA binding binding nucleic acid binding	-	protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	IPR010920	LSM domain superfamily	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	IPR047575	Sm domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	IPR022901	snRNP Sm-like, putative, archaea	Family
C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N]	IPR044641	Sm-like protein Lsm7/SmG	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.