4EMG

Crystal structure of SpLsm3

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)
B	d4emgb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
D	d4emgd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
E	d4emge_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
F	d4emgf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
G	d4emgg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
H	d4emgh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
I	d4emgi_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
J	d4emgj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
L	d4emgl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
M	d4emgm_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
N	d4emgn_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
A	d4emga_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
C	d4emgc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
K	d4emgk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
A	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8063453	4001809	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063454	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)
B	LSM	e4emgB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e4emgD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e4emgE2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e4emgF2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e4emgG2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e4emgH2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e4emgI2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e4emgJ2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e4emgL2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M	LSM	e4emgM2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
N	LSM	e4emgN2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A	LSM	e4emgA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e4emgC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e4emgK2	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)
B	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)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
M	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
N	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	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)
K	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, 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	Probable U6 snRNA-associated Sm-like protein LSm3	chromatin binding binding RNA binding organic cyclic compound binding nucleic acid binding telomerase RNA binding snRNA binding U2 snRNA binding	cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly non-membrane-bounded organelle assembly cellular process cellular component organization or biogenesis RNA folding RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly non-membrane-bounded organelle assembly cellular process cellular component organization or biogenesis RNA folding RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex precatalytic spliceosome spliceosomal snRNP complex U6 snRNP Sm-like protein family complex small nuclear ribonucleoprotein complex catalytic complex telomerase holoenzyme complex U2 snRNP catalytic step 2 spliceosome Lsm1-7-Pat1 complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex chromosome, telomeric repeat region chromosome chromosome, telomeric region chromosomal region Lsm2-8 complex U5 snRNP cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex P-body

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	IPR040002	U6 snRNA-associated Sm-like protein Lsm3	Family
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	IPR047575	Sm domain	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	IPR034105	Sm-like protein Lsm3	Domain

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.