7PDV | pdb_00007pdv

Crystal structure of RBM5 RRM1-zinc finger in complex with RNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth G]		e7pdvG1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)
C [auth E]		e7pdvE1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)
B [auth C]		e7pdvC1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)
A		e7pdvA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T:	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], E [auth G]	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
A, B [auth C], C [auth E], E [auth G]	PF00641	Zn-finger in Ran binding protein and others (Zn_ribbon_RanBP)	Zn-finger in Ran binding protein and others		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth F]	RNA (5'-R(PUPGPGPCPUPCPUPUPCPU)-3')	-	-	-
A, B [auth C], C [auth E], E [auth G]	RNA binding motif protein 5 isoform 1	RNA binding binding nucleic acid binding DNA binding mRNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process alternative mRNA splicing, via spliceosome RNA metabolic process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process RNA processing regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of cellular process alternative mRNA splicing, via spliceosome RNA metabolic process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process RNA processing regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing RNA splicing regulation of biological process biological regulation primary metabolic process 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 regulation of gene expression biosynthetic process RNA splicing, via transesterification reactions regulation of alternative mRNA splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular 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 negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process	sperm end piece membrane-bounded organelle cell projection cellular anatomical structure organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection intracellular organelle microtubule organizing center intracellular anatomical structure cytoskeleton sperm end piece membrane-bounded organelle cell projection cellular anatomical structure organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection intracellular organelle microtubule organizing center intracellular anatomical structure cytoskeleton membraneless organelle centriole intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol sperm principal piece perinuclear theca perinuclear region of cytoplasm sperm midpiece nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], E [auth G]	IPR013087	Zinc finger C2H2-type	Domain
A, B [auth C], C [auth E], E [auth G]	IPR034993	RNA-binding protein 5, RNA recognition motif 2	Domain
A, B [auth C], C [auth E], E [auth G]	IPR000467	G-patch domain	Domain
A, B [auth C], C [auth E], E [auth G]	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A, B [auth C], C [auth E], E [auth G]	IPR000504	RNA recognition motif domain	Domain
A, B [auth C], C [auth E], E [auth G]	IPR041591	OCRE domain	Domain
A, B [auth C], C [auth E], E [auth G]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B [auth C], C [auth E], E [auth G]	IPR001876	Zinc finger, RanBP2-type	Domain
A, B [auth C], C [auth E], E [auth G]	IPR034991	RNA-binding protein 5, RNA recognition motif 1	Domain
A, B [auth C], C [auth E], E [auth G]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], C [auth E], E [auth G]	Pharos: P52756	astrocytic tumor Gaucher disease metabolic syndrome X ovarian cancer Pick disease attention deficit hyperactivity disorder, inattentive type interstitial lung disease oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma progressive supranuclear palsy breast cancer malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia 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.