4RU2

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
Protein Family Annotation
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)
A	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)
E	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)
I	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)
M	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)
Q	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)
A	RRM_1_9	e4ru2A1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
C	RRM_1_9	e4ru2C1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
E	RRM_1_9	e4ru2E1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
G	RRM_1_9	e4ru2G1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
I	RRM_1_9	e4ru2I1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
K	RRM_1_9	e4ru2K1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
M	RRM_1_9	e4ru2M1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
O	RRM_1_9	e4ru2O1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)
Q	RRM_1_9	e4ru2Q1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_9	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
E	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)
I	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)
M	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)
Q	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
A, C, E, G, I A, C, E, G, I, K, M, O, Q	PF15519	linker between RRM2 and RRM3 domains in RBM39 protein (RBM39linker)	linker between RRM2 and RRM3 domains in RBM39 protein	A conserved linker between the second and the third RRM domain in human RBM39 (CAPER) protein, also present in other RNA binding proteins, especially those involved in RNA splicing. This linker was implicated in interactions with ESR1 and ESR2. Preli ...	A conserved linker between the second and the third RRM domain in human RBM39 (CAPER) protein, also present in other RNA binding proteins, especially those involved in RNA splicing. This linker was implicated in interactions with ESR1 and ESR2. Preliminary results from JCSG suggest that this is a structured domain with a well defined fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 RNA binding organic cyclic compound binding nucleic acid binding	RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance 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 cellular metabolic process regulation of macromolecule metabolic process regulation of RNA splicing mRNA metabolic process regulation of cellular biosynthetic 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen centrosome microtubule organizing center cytoskeleton centriolar satellite intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle protein-containing complex
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 organic cyclic compound 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 negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome organic substance biosynthetic process 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 cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound 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 cellular biosynthetic process RNA metabolic process negative regulation of mRNA metabolic process organic substance 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 regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic 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 positive regulation of biological process positive regulation of cellular metabolic 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 nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of gene expression positive regulation of RNA splicing positive regulation of cellular biosynthetic process 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 organonitrogen compound 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O, Q	IPR003954	RNA recognition motif domain, eukaryote	Domain
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	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
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

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.