3SWN | pdb_00003swn

Structure of the LSm657 Complex: An Assembly Intermediate of the LSm1 7 and LSm2 8 Rings

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)
I [auth Q]	d3swnq_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
C [auth B]	d3swnb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
F [auth E]	d3swne_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
L [auth T]	d3swnt_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
B [auth A]	d3swna_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
E [auth D]	d3swnd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
K [auth S]	d3swns_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	Fission yeast (Schizosaccharomyces pombe 972h- ) [TaxId: 284812 ],	SCOPe (2.08)
H [auth P]	d3swnp_	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)
I [auth Q]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063460	3000419	SCOP2B (2022-06-29)
C [auth B]	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8063459	4001809	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Superfamily	Sm-like ribonucleoproteins	8063460	3000419	SCOP2 (2022-06-29)
F [auth E]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063460	3000419	SCOP2B (2022-06-29)
L [auth T]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063460	3000419	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063480	3000419	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063480	3000419	SCOP2B (2022-06-29)
K [auth S]	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8063479	4001809	SCOP2 (2022-06-29)
K [auth S]	SCOP2 Superfamily	Sm-like ribonucleoproteins	8063480	3000419	SCOP2 (2022-06-29)
H [auth P]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063480	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)
I [auth Q]	LSM	e3swnQ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C [auth B]	LSM	e3swnB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F [auth E]	LSM	e3swnE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L [auth T]	LSM	e3swnT1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A [auth C]	LSM	e3swnC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G [auth O]	LSM	e3swnO1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D [auth F]	LSM	e3swnF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J [auth R]	LSM	e3swnR1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B [auth A]	LSM	e3swnA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E [auth D]	LSM	e3swnD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K [auth S]	LSM	e3swnS1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H [auth P]	LSM	e3swnP1	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)
I [auth Q]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C [auth B]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F [auth E]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L [auth T]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A [auth C]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G [auth O]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D [auth F]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J [auth R]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B [auth A]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E [auth D]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
K [auth S]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H [auth P]	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 B], F [auth E], I [auth Q], L [auth T]	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
A [auth C], D [auth F], G [auth O], J [auth R]	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
B [auth A], E [auth D], H [auth P], K [auth S]	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
C [auth B], F [auth E], I [auth Q], L [auth T]	U6 snRNA-associated Sm-like protein LSm6	RNA binding snRNA binding binding nucleic acid binding U2 snRNA binding poly-pyrimidine tract binding poly(U) RNA binding single-stranded RNA binding	ribonucleoprotein complex biogenesis telomerase holoenzyme complex assembly protein-containing complex organization protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis RNA splicing RNA metabolic process primary metabolic process ribonucleoprotein complex biogenesis telomerase holoenzyme complex assembly protein-containing complex organization protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis RNA splicing 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 tRNA metabolic process tRNA processing rRNA processing ribosomal small subunit biogenesis ribosome biogenesis maturation of SSU-rRNA rRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen spliceosomal snRNP complex protein-containing complex U6 snRNP nuclear protein-containing complex Sm-like protein family complex small nuclear ribonucleoprotein complex ribonucleoprotein complex catalytic complex telomerase holoenzyme complex U2 snRNP Lsm2-8 complex spliceosomal complex sno(s)RNA-containing ribonucleoprotein complex U5 snRNP cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex P-body Lsm1-7-Pat1 complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex
A [auth C], D [auth F], G [auth O], J [auth R]	U6 snRNA-associated Sm-like protein LSm7	RNA binding snRNA binding binding nucleic acid binding U2 snRNA binding poly-pyrimidine tract binding poly(U) RNA binding single-stranded RNA binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA splicing nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing ribonucleoprotein complex biogenesis telomerase holoenzyme complex assembly protein-containing complex organization protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis rRNA processing ribosome biogenesis rRNA metabolic process tRNA metabolic process tRNA processing	membrane-bounded organelle spliceosomal snRNP complex protein-containing complex U6 snRNP intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex membrane-bounded organelle spliceosomal snRNP complex protein-containing complex U6 snRNP intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex catalytic complex telomerase holoenzyme complex U2 snRNP catalytic step 2 spliceosome spliceosomal complex Lsm2-8 complex cytoplasm cytosol U5 snRNP spliceosomal tri-snRNP complex Lsm1-7-Pat1 complex U4/U6 x U5 tri-snRNP complex U2-type spliceosomal complex prespliceosome U2-type prespliceosome
B [auth A], E [auth D], H [auth P], K [auth S]	U6 snRNA-associated Sm-like protein LSm5	RNA binding snRNA binding binding nucleic acid binding U2 snRNA binding poly-pyrimidine tract binding poly(U) RNA binding single-stranded RNA binding	ribonucleoprotein complex biogenesis telomerase holoenzyme complex assembly protein-containing complex organization protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis RNA splicing RNA metabolic process primary metabolic process ribonucleoprotein complex biogenesis telomerase holoenzyme complex assembly protein-containing complex organization protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis RNA splicing 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 rRNA processing ribosome biogenesis rRNA metabolic process tRNA metabolic process tRNA processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen spliceosomal snRNP complex protein-containing complex U6 snRNP nuclear protein-containing complex Sm-like protein family complex small nuclear ribonucleoprotein complex ribonucleoprotein complex catalytic complex telomerase holoenzyme complex U2 snRNP Lsm2-8 complex spliceosomal complex sno(s)RNA-containing ribonucleoprotein complex U5 snRNP Lsm1-7-Pat1 complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B], F [auth E], I [auth Q], L [auth T]	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
C [auth B], F [auth E], I [auth Q], L [auth T]	IPR047575	Sm domain	Domain
C [auth B], F [auth E], I [auth Q], L [auth T]	IPR016487	Sm-like protein Lsm6/SmF	Family
C [auth B], F [auth E], I [auth Q], L [auth T]	IPR010920	LSM domain superfamily	Homologous Superfamily
A [auth C], D [auth F], G [auth O], J [auth R]	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A [auth C], D [auth F], G [auth O], J [auth R]	IPR047575	Sm domain	Domain
A [auth C], D [auth F], G [auth O], J [auth R]	IPR044641	Sm-like protein Lsm7/SmG	Family
A [auth C], D [auth F], G [auth O], J [auth R]	IPR010920	LSM domain superfamily	Homologous Superfamily
A [auth C], D [auth F], G [auth O], J [auth R]	IPR017132	Sm-like protein Lsm7	Family
B [auth A], E [auth D], H [auth P], K [auth S]	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
B [auth A], E [auth D], H [auth P], K [auth S]	IPR047575	Sm domain	Domain
B [auth A], E [auth D], H [auth P], K [auth S]	IPR033871	Sm-like protein LSm5	Domain
B [auth A], E [auth D], H [auth P], K [auth S]	IPR010920	LSM domain superfamily	Homologous Superfamily

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.