3H2V

Human raver1 RRM1 domain in complex with human vinculin tail domain Vt

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)
A	d3h2va_	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3h2vb_	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3h2vc_	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3h2vd_	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3h2ve1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3h2ve2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3h2vf1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3h2vf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3h2vg1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3h2vg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3h2vh1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3h2vh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
E	SCOP2 Family	Canonical RBD	8088419	4000236	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	RNA-binding domain RBD	8088420	3000110	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	RNA-binding domain RBD	8088420	3000110	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA-binding domain RBD	8088420	3000110	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RNA-binding domain RBD	8088420	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	PF01044	e3h2vA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: PF01044	ECOD (1.6)
B	PF01044	e3h2vB1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: PF01044	ECOD (1.6)
C	PF01044	e3h2vC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: PF01044	ECOD (1.6)
D	PF01044	e3h2vD1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: PF01044	ECOD (1.6)
E	PF00076	e3h2vE1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: PF00076	ECOD (1.6)
F	PF00076	e3h2vF1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: PF00076	ECOD (1.6)
G	PF00076	e3h2vG1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: PF00076	ECOD (1.6)
H	PF00076	e3h2vH1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: PF00076	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.230	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Alpha-catenin/vinculin-like	CATH (4.3.0)
B	1.20.120.230	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Alpha-catenin/vinculin-like	CATH (4.3.0)
C	1.20.120.230	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Alpha-catenin/vinculin-like	CATH (4.3.0)
D	1.20.120.230	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Alpha-catenin/vinculin-like	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)
F	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)
H	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, B, C, D	PF01044	Vinculin family (Vinculin)	Vinculin family	-	Family
E, F, G, H	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, B, C, D	Vinculin	protein binding binding alpha-catenin binding cell adhesion molecule binding cadherin binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding dystroglycan binding cytoskeletal protein binding actin binding structural molecule activity beta-catenin binding	regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization cellular process regulation of focal adhesion assembly regulation of cell-substrate junction assembly cell-cell adhesion epithelial cell-cell adhesion lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly lamellipodium organization cell projection assembly developmental process tissue morphogenesis anatomical structure morphogenesis epithelium development anatomical structure development morphogenesis of an epithelium tissue development multicellular organismal process regulation of body fluid levels wound healing response to stimulus homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation apical junction assembly cell-cell junction assembly cell-cell junction organization negative regulation of locomotion regulation of cell motility negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion axon extension axonogenesis cellular developmental process developmental growth plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation system development neuron projection extension developmental cell growth growth nervous system development axon development cell morphogenesis involved in neuron differentiation developmental growth involved in morphogenesis generation of neurons neuron development adherens junction organization adherens junction assembly protein localization localization cellular localization protein localization to cell surface cellular macromolecule localization macromolecule localization regulation of localization regulation of protein localization regulation of protein localization to cell-cell junction regulation of protein localization to adherens junction protein localization to adherens junction protein localization to cell-cell junction regulation of cellular localization protein localization to cell junction regulation of establishment of endothelial barrier regulation of developmental process endothelium development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development regulation of endothelial cell development regulation of multicellular organismal process regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation epithelial cell development establishment of endothelial barrier maintenance of blood-brain barrier multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis	intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton terminal web cytoplasm non-membrane-bounded organelle intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton terminal web cytoplasm non-membrane-bounded organelle cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol sarcolemma plasma membrane membrane costamere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex cluster of actin-based cell projections brush border adherens junction intercalated disc fascia adherens cell-cell contact zone cell-substrate junction desmosome inner dense plaque of desmosome vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen cytoplasmic vesicle organelle lumen specific granule lumen secretory granule secretory vesicle specific granule podosome podosome ring focal adhesion outer dense plaque of desmosome membrane microdomain membrane raft apical junction complex zonula adherens ficolin-1-rich granule ficolin-1-rich granule lumen protein-containing complex cell projection
E, F, G, H	Raver-1	RNA binding binding organic cyclic compound binding nucleic acid binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017997	Vinculin	Family
A, B, C, D	IPR036723	Alpha-catenin/vinculin-like superfamily	Homologous Superfamily
A, B, C, D	IPR006077	Vinculin/alpha-catenin	Family
A, B, C, D	IPR000633	Vinculin, conserved site	Conserved Site
E, F, G, H	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
E, F, G, H	IPR034633	Ribonucleoprotein PTB-binding 1, RNA recognition motif 1	Domain
E, F, G, H	IPR000504	RNA recognition motif domain	Domain
E, F, G, H	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
E, F, G, H	IPR034635	Ribonucleoprotein PTB-binding 1, RNA recognition motif 3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P18206	dilated cardiomyopathy 1W hypertrophic cardiomyopathy 15 dilated cardiomyopathy osteoporosis acute coronary syndrome cardiomyopathy hypertrophic cardiomyopathy malignant ependymoma ovarian cancer spondyloarthropathy Crohn disease familial isolated dilated cardiomyopathy lung carcinoma malignant pancreatic neoplasm Osteoporosis, Age-Related dilated cardiomyopathy 1W hypertrophic cardiomyopathy 15 dilated cardiomyopathy osteoporosis acute coronary syndrome cardiomyopathy hypertrophic cardiomyopathy malignant ependymoma ovarian cancer spondyloarthropathy Crohn disease familial isolated dilated cardiomyopathy lung carcinoma malignant pancreatic neoplasm Osteoporosis, Age-Related pancreatic ductal adenocarcinoma subependymal giant cell astrocytoma astrocytic tumor Charcot-Marie-Tooth disease diabetes mellitus familial dilated cardiomyopathy glioblastoma inflammatory bowel disease malignant colon neoplasm medulloblastoma tuberculosis atypical teratoid rhabdoid tumor familial hypertrophic cardiomyopathy lung cancer
E, F, G, H	Pharos: Q8IY67	ankylosing spondylitis Hashimoto thyroiditis juvenile idiopathic arthritis primary biliary cholangitis systemic sclerosis breast carcinoma hypothyroidism multiple sclerosis psoriasis ulcerative colitis Crohn disease inflammatory bowel disease myositis systemic lupus erythematosus

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 R01GM133198.