1D3B | pdb_00001d3b

CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP DOMAIN AT 2.0A RESOLUTION

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d1d3bl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	B core SNRNP protein	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d1d3bj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	B core SNRNP protein	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1d3bh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	B core SNRNP protein	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1d3bf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	B core SNRNP protein	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1d3bd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	B core SNRNP protein	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1d3bb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	B core SNRNP protein	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d1d3bk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	D3 core SNRNP protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d1d3bi_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	D3 core SNRNP protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1d3bg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	D3 core SNRNP protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1d3be_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	D3 core SNRNP protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1d3bc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	D3 core SNRNP protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1d3ba_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	D3 core SNRNP protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041747	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041747	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041747	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041747	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041747	3000419	SCOP2B (2022-06-29)
B	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8029368	4001809	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Sm-like ribonucleoproteins	8041747	3000419	SCOP2 (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041751	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041751	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041751	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041751	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8041751	3000419	SCOP2B (2022-06-29)
A	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8029372	4001809	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sm-like ribonucleoproteins	8041751	3000419	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	LSM	e1d3bL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e1d3bJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e1d3bH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e1d3bF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e1d3bD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e1d3bB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e1d3bK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e1d3bI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e1d3bG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e1d3bE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e1d3bC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A	LSM	e1d3bA1	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)
L	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)
H	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)
D	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)
K	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)
G	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)
C	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	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, C, E, G, I A, C, E, G, I, K	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
B, D, F, H, J B, D, F, H, J, L	PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)	RNA binding binding nucleic acid binding histone pre-mRNA DCP binding U1 snRNP binding ribonucleoprotein complex binding snRNP binding protein-containing complex binding telomerase RNA binding U2 snRNP binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 7-methylguanosine cap hypermethylation RNA capping macromolecule methylation RNA modification methylation macromolecule modification RNA 5'-end processing RNA methylation protein methylation protein alkylation protein metabolic process protein modification process	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 intracellular organelle U4 snRNP cellular anatomical structure 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 intracellular organelle U4 snRNP cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex catalytic complex telomerase holoenzyme complex U2 snRNP catalytic step 2 spliceosome spliceosomal complex histone pre-mRNA 3'end processing complex cytoplasm cytosol U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex U1 snRNP membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen SMN-Sm protein complex U2-type spliceosomal complex U2-type precatalytic spliceosome precatalytic spliceosome methylosome methyltransferase complex transferase complex U12-type spliceosomal complex U5 snRNP U7 snRNP prespliceosome U2-type prespliceosome U2-type catalytic step 2 spliceosome
A, C, E, G, I A, C, E, G, I, K	PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)	RNA binding binding nucleic acid binding histone pre-mRNA DCP binding snRNA binding U7 snRNA binding telomerase RNA binding protein binding enzyme binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 7-methylguanosine cap hypermethylation RNA capping macromolecule methylation RNA modification methylation macromolecule modification RNA 5'-end processing RNA methylation protein methylation protein alkylation protein metabolic process protein modification process	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 intracellular organelle U4 snRNP cellular anatomical structure 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 intracellular organelle U4 snRNP cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex pICln-Sm protein complex cytoplasm spliceosomal complex precatalytic spliceosome catalytic complex telomerase holoenzyme complex U2 snRNP catalytic step 2 spliceosome cytosol U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex U1 snRNP membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen SMN-Sm protein complex U2-type spliceosomal complex U2-type precatalytic spliceosome methylosome methyltransferase complex transferase complex U12-type spliceosomal complex U5 snRNP U7 snRNP commitment complex intracellular membraneless organelle nuclear body membraneless organelle U2-type catalytic step 2 spliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
B, D, F, H, J B, D, F, H, J, L	IPR017131	Small ribonucleoprotein associated, SmB/SmN	Family
B, D, F, H, J B, D, F, H, J, L	IPR047575	Sm domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR010920	LSM domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR027141	Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3	Family
A, C, E, G, I A, C, E, G, I, K	IPR034099	Small nuclear ribonucleoprotein Sm D3	Family
A, C, E, G, I A, C, E, G, I, K	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A, C, E, G, I A, C, E, G, I, K	IPR047575	Sm domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR010920	LSM domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L	Pharos: P14678	cerebrocostomandibular syndrome intellectual disability ovarian cancer atypical teratoid rhabdoid tumor dermatomyositis Disease Progression glioblastoma invasive ductal breast carcinoma malignant glioma medulloblastoma plasma cell myeloma diabetes mellitus gastric cancer hereditary diffuse gastric adenocarcinoma large cell medulloblastoma cerebrocostomandibular syndrome intellectual disability ovarian cancer atypical teratoid rhabdoid tumor dermatomyositis Disease Progression glioblastoma invasive ductal breast carcinoma malignant glioma medulloblastoma plasma cell myeloma diabetes mellitus gastric cancer hereditary diffuse gastric adenocarcinoma large cell medulloblastoma malignant mesothelioma osteosarcoma psoriasis gastric neoplasm lymphoplasmacytic lymphoma
A, C, E, G, I A, C, E, G, I, K	Pharos: P62318	carcinoma Mammary Neoplasms, Experimental HIV infectious disease sarcomatoid carcinoma acne lymphoplasmacytic lymphoma ovarian cancer undifferentiated carcinoma medulloblastoma plasma cell myeloma dermatomyositis lung cancer mammary neoplasms, animal non-alcoholic fatty liver disease

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.