4JHP

The crystal structure of the RPGR RCC1-like domain in complex with PDE6D

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d4jhpb_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	RhoGDI-like	GMP-PDE delta	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)
A [auth B]	SCOP2B Superfamily	E set domains	8055021	3000070	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 [auth B]	GMP_PDE_delta	e4jhpB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GMP_PDE_delta	ECOD (1.6)
B [auth C]	RCC1	e4jhpC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: RCC1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.70.50.40	Mainly Beta	Distorted Sandwich	Coagulation Factor XIII	Chain A, domain 1	CATH (4.3.0)
B [auth C]	2.130.10.30	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF05351	GMP-PDE, delta subunit (GMP_PDE_delta)	GMP-PDE, delta subunit	-	Family
B [auth C]	PF00415	Regulator of chromosome condensation (RCC1) repeat (RCC1)	Regulator of chromosome condensation (RCC1) repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	GTPase regulator activity enzyme regulator activity GTPase inhibitor activity molecular function inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme inhibitor activity small GTPase binding protein binding binding enzyme binding GTPase binding	multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception response to stimulus	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane cell projection cilium plasma membrane bounded cell projection cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytosol
B [auth C]	X-linked retinitis pigmentosa GTPase regulator	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity RNA binding binding organic cyclic compound binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity RNA binding binding organic cyclic compound binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport plasma membrane bounded cell projection organization cell projection organization protein-containing complex localization cellular component organization organelle organization microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process cellular component organization or biogenesis cilium organization intraciliary transport multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal response to stimulus organelle assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cell projection assembly	membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cell projection cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection ciliary basal body non-motile cilium 9+0 non-motile cilium neuron projection photoreceptor outer segment photoreceptor cell cilium

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR008015	GMP phosphodiesterase, delta subunit	Domain
A [auth B]	IPR017287	Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit	Family
A [auth B]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth B]	IPR037036	GMP phosphodiesterase, delta subunit superfamily	Homologous Superfamily
B [auth C]	IPR000408	Regulator of chromosome condensation, RCC1	Repeat
B [auth C]	IPR009091	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: O43924	orofaciodigital syndrome type 6 Joubert syndrome 22 atrial fibrillation Ciliopathies ovarian cancer breast cancer coloboma Sjogren syndrome Joubert syndrome polydactyly
B [auth C]	Pharos: Q92834	retinitis pigmentosa retinal degeneration primary ciliary dyskinesia-retinitis pigmentosa syndrome cone-rod dystrophy inherited retinal dystrophy macular degeneration, X-linked atrophic X-linked cone-rod dystrophy 1 retinitis pigmentosa 3 achromatopsia primary ciliary dyskinesia age-related macular degeneration hearing loss disorder non-small cell lung carcinoma Polynesian Bronchiectasis psoriasis retinitis pigmentosa retinal degeneration primary ciliary dyskinesia-retinitis pigmentosa syndrome cone-rod dystrophy inherited retinal dystrophy macular degeneration, X-linked atrophic X-linked cone-rod dystrophy 1 retinitis pigmentosa 3 achromatopsia primary ciliary dyskinesia age-related macular degeneration hearing loss disorder non-small cell lung carcinoma Polynesian Bronchiectasis psoriasis tuberculosis breast cancer cone dystrophy lung cancer malignant ependymoma osteosarcoma choroideremia Leber congenital amaurosis macular degeneration night blindness pituitary cancer respiratory tract infectious disease Usher syndrome blindness (disorder) ciliopathy lung adenocarcinoma

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.