1A9N

CRYSTAL STRUCTURE OF THE SPLICEOSOMAL U2B''-U2A' PROTEIN COMPLEX BOUND TO A FRAGMENT OF U2 SMALL NUCLEAR RNA

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)
D [auth C]	d1a9nc_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	U2A'-like	Spliceosomal U2 small nuclear ribonucleoprotein A' / U2A' / Lea1 protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1a9na_	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	U2A'-like	Spliceosomal U2 small nuclear ribonucleoprotein A' / U2A' / Lea1 protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d1a9nb_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Spliceosomal U2 small nuclear ribonucleoprotein B' / U2B' / Msl1 protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d1a9nd_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Spliceosomal U2 small nuclear ribonucleoprotein B' / U2B' / Msl1 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)
D [auth C]	SCOP2B Superfamily	L domain-like	8043993	3001010	SCOP2B (2022-06-29)
C [auth A]	SCOP2 Family	U2A'-like	8031615	4003542	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	L domain-like	8043993	3001010	SCOP2 (2022-06-29)
E [auth B]	SCOP2 Family	Canonical RBD	8022947	4000236	SCOP2 (2022-06-29)
E [auth B]	SCOP2 Superfamily	RNA-binding domain, RBD	8035327	3000110	SCOP2 (2022-06-29)
F [auth D]	SCOP2B Superfamily	RNA-binding domain, RBD	8035327	3000110	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)
D [auth C]	LRR_9	e1a9nC1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_9	ECOD (1.6)
C [auth A]	LRR_9	e1a9nA1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_9	ECOD (1.6)
E [auth B]	RRM_1_2	e1a9nB2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_2	ECOD (1.6)
F [auth D]	RRM_1_2	e1a9nD2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C [auth A]	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
E [auth B]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
F [auth D]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth B], F [auth D]	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Q], B [auth R]	RNA (5'-R(CPCPUPGPGPUPAPUPUPGPCPAPGPUPAPCPCPUPCPCPAPGP* GP*U)-3')	-	-	-
C [auth A], D [auth C]	U2A'	RNA binding snRNA binding binding nucleic acid binding U2 snRNA binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component organization cellular component biogenesis spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization U2-type prespliceosome assembly	membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen Sm-like protein family complex small nuclear ribonucleoprotein complex spliceosomal snRNP complex U2 snRNP catalytic step 2 spliceosome catalytic complex U2-type precatalytic spliceosome precatalytic spliceosome U2-type catalytic step 2 spliceosome
E [auth B], F [auth D]	SPLICEOSOMAL U2B''	RNA binding snRNA binding binding nucleic acid binding U1 snRNA binding ribonucleoprotein complex binding snRNP binding protein-containing complex binding	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 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 cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component organization cellular component biogenesis spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization U2-type prespliceosome assembly	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule membrane-bounded organelle U2-type spliceosomal complex protein-containing complex nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule membrane-bounded organelle U2-type spliceosomal complex protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle spliceosomal complex ribonucleoprotein complex membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen spliceosomal snRNP complex Sm-like protein family complex small nuclear ribonucleoprotein complex U2 snRNP catalytic step 2 spliceosome catalytic complex U2-type precatalytic spliceosome precatalytic spliceosome nucleolus fibrillar center U1 snRNP U2-type catalytic step 2 spliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth C]	IPR001611	Leucine-rich repeat	Repeat
C [auth A], D [auth C]	IPR003603	U2A'/phosphoprotein 32 family A, C-terminal	Domain
C [auth A], D [auth C]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C [auth A], D [auth C]	IPR044640	U2 small nuclear ribonucleoprotein A'	Family
E [auth B], F [auth D]	IPR034562	U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2	Domain
E [auth B], F [auth D]	IPR000504	RNA recognition motif domain	Domain
E [auth B], F [auth D]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
E [auth B], F [auth D]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
E [auth B], F [auth D]	IPR034564	U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth B], F [auth D]	Pharos: P08579	breast carcinoma medulloblastoma colorectal cancer lung cancer

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.