1LNX | pdb_00001lnx

Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221)

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)
A	d1lnxa1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
A	d1lnxa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
B	d1lnxb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
C	d1lnxc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
D	d1lnxd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
E	d1lnxe_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
F	d1lnxf1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
F	d1lnxf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)
G	d1lnxg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrobaculum aerophilum ) [TaxId: 13773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033782	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)
A	LSM	e1lnxA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e1lnxB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e1lnxC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e1lnxD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e1lnxE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e1lnxF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e1lnxG1	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)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G	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
A, B, C, D, E A, B, C, D, E, F, G	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, B, C, D, E A, B, C, D, E, F, G	small nuclear ribonucleoprotein homolog (Sm-like)	RNA binding binding nucleic acid binding	-	protein-containing complex ribonucleoprotein complex Sm-like protein family complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR010920	LSM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR047575	Sm domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR022901	snRNP Sm-like, putative, archaea	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR044642	U6 snRNA-associated Sm-like protein Lsm1/8	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.