5MKI | pdb_00005mki

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii

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)
N	d5mkin_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
M	d5mkim_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
L	d5mkil_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
K	d5mkik_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
J	d5mkij_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
I	d5mkii_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
H	d5mkih_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
G	d5mkig_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
F	d5mkif_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
E	d5mkie_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
D	d5mkid_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
C	d5mkic_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
B	d5mkib_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
A	d5mkia_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
H	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8063439	4001809	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	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)
N	LSM	e5mkiN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M	LSM	e5mkiM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e5mkiL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e5mkiK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e5mkiJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e5mkiI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e5mkiH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e5mkiG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e5mkiF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e5mkiE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e5mkiD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e5mkiC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e5mkiB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A	LSM	e5mkiA1	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)
N	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
M	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
L	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
K	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
J	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
I	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
G	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, 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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	Like-Sm ribonucleoprotein core	RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	-	protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR010920	LSM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR047575	Sm domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR022901	snRNP Sm-like, putative, archaea	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.