1N9R

Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122

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	d1n9ra_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1n9rb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1n9rc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1n9rd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1n9re_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d1n9rf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d1n9rg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Small nuclear ribonucleoprotein F, Smf	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins SNRNP	8031325	4001809	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sm-like ribonucleoproteins	8043703	3000419	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043703	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043703	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043703	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043703	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043703	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043703	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	e1n9rA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e1n9rB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e1n9rC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e1n9rD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e1n9rE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e1n9rF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e1n9rG1	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 F	RNA binding binding organic cyclic compound binding nucleic acid binding splicing factor binding protein binding poly-pyrimidine tract binding poly(U) RNA binding single-stranded RNA binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly organic substance metabolic process protein-containing complex assembly organic substance biosynthetic process ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly organic substance metabolic process protein-containing complex assembly organic substance biosynthetic process cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization cellular metabolic process primary metabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process RNA splicing, via transesterification reactions U2-type prespliceosome assembly mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process spliceosomal snRNP assembly mRNA splice site recognition mRNA 5'-splice site recognition mRNA cis splicing, via spliceosome RNA capping 7-methylguanosine cap hypermethylation macromolecule methylation RNA modification methylation macromolecule modification RNA 5'-end processing RNA methylation	membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle U4 snRNP small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle U4 snRNP small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex pICln-Sm protein complex cytoplasm U2 snRNP catalytic step 2 spliceosome catalytic complex spliceosomal complex U4/U6 snRNP U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex U1 snRNP U5 snRNP U2-type spliceosomal complex commitment complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR016487	Sm-like protein Lsm6/SmF	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR034100	Small nuclear ribonucleoprotein F	Family
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	IPR047575	Sm domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR010920	LSM domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.