4RU2 | pdb_00004ru2

Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Mus musculus at 2.20 A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
Q	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
K	SCOP2 Family	Canonical RBD	8065228	4000236	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8065229	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)
Q	Beta-Casp	e4ru2Q1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
O	Beta-Casp	e4ru2O1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
M	Beta-Casp	e4ru2M1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
K	Chlor_dismutase	e4ru2K1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Chlor_dismutase	ECOD (v294.1)
I	Beta-Casp	e4ru2I1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
G	Beta-Casp	e4ru2G1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
E	Beta-Casp	e4ru2E1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
C	Beta-Casp	e4ru2C1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
A	Beta-Casp	e4ru2A1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
Q	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
O	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
M	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
K	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
I	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
G	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
E	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
C	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

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, N, P, R	Splicing factor U2AF 65 kDa subunit	poly-pyrimidine tract binding RNA binding binding nucleic acid binding single-stranded RNA binding molecular function inhibitor activity molecular function regulator activity pre-mRNA binding pre-mRNA 3'-splice site binding protein binding enzyme binding C2H2 zinc finger domain binding protein domain specific binding	regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process negative regulation of metabolic process primary metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of mRNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of mRNA processing RNA splicing biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process negative regulation of RNA splicing RNA splicing, via transesterification reactions negative regulation of biosynthetic process mRNA splicing, via spliceosome cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process 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 positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of RNA splicing negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen protein-containing complex Prp19 complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex U2AF complex U2-type spliceosomal complex commitment complex prespliceosome U2-type prespliceosome
A, C, E, G, I A, C, E, G, I, K, M, O, Q	RNA-binding protein 39 (RBM39)	U1 snRNP binding ribonucleoprotein complex binding snRNP binding protein-containing complex binding binding RS domain binding protein binding protein domain specific binding transcription coactivator activity transcription regulator activity transcription coregulator activity RNA binding nucleic acid 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 regulation of cellular process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing mRNA metabolic process regulation of gene expression RNA splicing, via transesterification reactions mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen centrosome microtubule organizing center cytoskeleton centriolar satellite microtubule cytoskeleton protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P, R	IPR006529	U2 snRNP auxilliary factor, large subunit, splicing factor	Family
B, D, F, H, J B, D, F, H, J, L, N, P, R	IPR000504	RNA recognition motif domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P, R	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P, R	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR000504	RNA recognition motif domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR006509	Splicing factor, RBM39-like	Family
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR003954	RNA recognition motif domain, eukaryotic-type	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR029123	Splicing factor RBM39, linker	Domain

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.