1SYX | pdb_00001syx

The crystal structure of a binary U5 snRNP complex

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)
F	d1syxf_	Alpha and beta proteins (a+b)	GYF/BRK domain-like	GYF domain	GYF domain	GYF domain from cd2bp2 protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth D]	d1syxd_	Alpha and beta proteins (a+b)	GYF/BRK domain-like	GYF domain	GYF domain	GYF domain from cd2bp2 protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d1syxb_	Alpha and beta proteins (a+b)	GYF/BRK domain-like	GYF domain	GYF domain	GYF domain from cd2bp2 protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth E]	d1syxe_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	spliceosomal protein U5-15Kd	spliceosomal protein U5-15Kd	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d1syxc_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	spliceosomal protein U5-15Kd	spliceosomal protein U5-15Kd	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1syxa_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	spliceosomal protein U5-15Kd	spliceosomal protein U5-15Kd	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)
F	SCOP2B Superfamily	GYF domain-like	8032414	3001702	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	GYF domain-like	8032414	3001702	SCOP2B (2022-06-29)
D [auth B]	SCOP2 Family	GYF domain-like	8020034	4001496	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	GYF domain-like	8032414	3001702	SCOP2 (2022-06-29)
C [auth E]	SCOP2B Superfamily	Thioredoxin-like	8044390	3000031	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Thioredoxin-like	8044390	3000031	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin-like	8044390	3000031	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)
F	Nup35_RRM	e1syxF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Nup35_RRM	ECOD (v294.1)
E [auth D]	Nup35_RRM	e1syxD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Nup35_RRM	ECOD (v294.1)
D [auth B]	GYF	e1syxB1	A: a+b two layers	X: GYF/BRK domain-like	H: GYF domain	T: GYF domain	F: GYF	ECOD (v294.1)
C [auth E]	ECH_1	e1syxE1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (v294.1)
B [auth C]	ECH_1	e1syxC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (v294.1)
A	ECH_1	e1syxA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: ECH_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
E [auth D]	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D [auth B]	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C [auth E]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B [auth C]	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B], E [auth D], F	PF02213	GYF domain (GYF)	GYF domain	The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein Swiss:O95400.	Domain
A, B [auth C], C [auth E]	PF02966	Mitosis protein DIM1 (DIM1)	Mitosis protein DIM1		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth B], E [auth D], F	CD2 antigen cytoplasmic tail-binding protein 2	ribonucleoprotein complex binding protein-containing complex binding binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly 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 mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center organelle membraneless organelle nuclear lumen U5 snRNP spliceosomal snRNP complex protein-containing complex nuclear protein-containing complex Sm-like protein family complex small nuclear ribonucleoprotein complex ribonucleoprotein complex nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule
A, B [auth C], C [auth E]	Spliceosomal U5 snRNP-specific 15 kDa protein	-	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 mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process cell division	membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle U2-type precatalytic spliceosome intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex precatalytic spliceosome membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle U2-type precatalytic spliceosome intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex precatalytic spliceosome cytoplasm cytosol U5 snRNP spliceosomal snRNP complex Sm-like protein family complex small nuclear ribonucleoprotein complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth B], E [auth D], F	IPR003169	GYF domain	Domain
D [auth B], E [auth D], F	IPR035445	GYF-like domain superfamily	Homologous Superfamily
D [auth B], E [auth D], F	IPR039905	CD2 antigen cytoplasmic tail-binding protein 2/Lin1	Family
A, B [auth C], C [auth E]	IPR004123	Dim1 family	Family
A, B [auth C], C [auth E]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B], E [auth D], F	Pharos: O95400	diabetes mellitus osteosarcoma ovarian cancer
A, B [auth C], C [auth E]	Pharos: P83876	Burn-Mckeown syndrome choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome astrocytic tumor choanal atresia glioblastoma malignant ependymoma ovarian cancer atypical teratoid rhabdoid tumor intellectual disability malignant glioma plasma cell myeloma diabetes mellitus lung cancer osteosarcoma psoriasis

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.