7F6J | pdb_00007f6j

Crystal structure of the PDZD8 coiled-coil domain - Rab7 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057260	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057260	3002022	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)
B	Ras	e7f6jB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
A	Ras	e7f6jA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	PDZ domain-containing protein 8	binding lipid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular component organization organelle organization cellular process cellular component organization or biogenesis cytoskeleton organization localization transport macromolecule localization lipid localization lipid transport establishment of localization organelle localization by membrane tethering mitochondrion-endoplasmic reticulum membrane tethering organelle localization cellular component organization organelle organization cellular process cellular component organization or biogenesis cytoskeleton organization localization transport macromolecule localization lipid localization lipid transport establishment of localization organelle localization by membrane tethering mitochondrion-endoplasmic reticulum membrane tethering organelle localization membrane docking developmental process anatomical structure morphogenesis regulation of biological process regulation of developmental process anatomical structure development biological regulation cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis mitochondrial calcium ion homeostasis inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site membrane organelle subcompartment endomembrane system endoplasmic reticulum subcompartment membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site membrane organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane
A, B	Ras-related protein Rab-7a	small GTPase binding protein binding binding enzyme binding GTPase binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein-containing complex binding retromer complex binding small GTPase binding protein binding binding enzyme binding GTPase binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein-containing complex binding retromer complex binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding G protein activity molecular function regulator activity	cellular component organization organelle organization cellular process cellular component organization or biogenesis phagosome maturation homeostatic process biological regulation intracellular pH reduction regulation of intracellular pH phagosome acidification cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH cellular component organization organelle organization cellular process cellular component organization or biogenesis phagosome maturation homeostatic process biological regulation intracellular pH reduction regulation of intracellular pH phagosome acidification cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis regulation of cellular pH intracellular monoatomic ion homeostasis cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell vesicle localization establishment of organelle localization organelle localization establishment of vesicle localization establishment of protein localization nitrogen compound transport establishment of protein localization to plasma membrane endocytic recycling intracellular protein localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport protein transport macromolecule localization intracellular protein transport multicellular organismal process multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption catabolic process lipophagy macroautophagy autophagy metabolic process process utilizing autophagic mechanism membrane docking protein to membrane docking import into cell membrane fusion organelle membrane fusion vesicle organization cellular component biogenesis lysosome organization cellular component assembly phagolysosome assembly phagocytosis membrane organization vacuole organization organelle assembly lytic vacuole organization phagosome-lysosome fusion organelle fusion endocytosis vesicle fusion endosome to lysosome transport lysosomal transport vacuolar transport autophagosome assembly autophagosome organization exosomal secretion regulation of localization regulation of cellular process negative regulation of biological process negative regulation of transport secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of exosomal secretion negative regulation of cellular process negative regulation of secretion by cell regulation of biological process secretion regulation of transport regulation of exosomal secretion export from cell regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis extracellular vesicle biogenesis regulation of exocytosis positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process synaptic vesicle cycle vesicle-mediated transport in synapse synaptic vesicle endosomal processing synaptic vesicle recycling via endosome synaptic vesicle recycling vesicle budding from membrane regulation of cellular component organization regulation of endosome organization endosome organization endomembrane system organization negative regulation of cellular component organization negative regulation of intralumenal vesicle formation intralumenal vesicle formation regulation of organelle organization negative regulation of organelle organization negative regulation of endosome organization regulation of intralumenal vesicle formation lipid catabolic process lipid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus exit from host cell viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of protein localization to vacuole neurotransmitter receptor transport, postsynaptic endosome to lysosome neurotransmitter receptor transport protein localization to vacuole protein-containing complex localization protein localization to lysosome establishment of protein localization to organelle protein localization to organelle positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis positive regulation of secretion positive regulation of cellular component biogenesis regulation of cellular component biogenesis positive regulation of transport cellular response to stimulus signaling negative regulation of signaling negative regulation of ERBB signaling pathway regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway epidermal growth factor catabolic process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication protein targeting protein targeting to lysosome protein targeting to vacuole vesicle-mediated transport between endosomal compartments early endosome to late endosome transport regulation of viral process positive regulation of viral process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope mitochondrial envelope cytoplasm organelle membrane cytosol endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome synapse cell junction glutamatergic synapse vacuolar membrane autophagosome membrane vacuole autophagosome phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle lytic vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle pigment granule chitosome melanosome melanosome membrane pigment granule membrane presynaptic endosome lamellar body secretory granule alveolar lamellar body cell periphery plasma membrane phagophore assembly site membrane phagophore assembly site secretory granule membrane lipid droplet membraneless organelle intracellular membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
C	IPR031468	Synaptotagmin-like mitochondrial-lipid-binding domain	Domain
C	IPR041489	PDZ domain 6	Domain
C	IPR036034	PDZ superfamily	Homologous Superfamily
C	IPR039275	PDZ domain-containing protein 8	Family
C	IPR001478	PDZ domain	Domain
C	IPR046349	C1-like domain superfamily	Homologous Superfamily
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q8NEN9	breast cancer malignant colon neoplasm osteosarcoma peripheral arterial disease spina bifida large cell medulloblastoma malignant glioma ovarian cancer psoriasis tuberculosis lung cancer medulloblastoma pancreatic ductal adenocarcinoma Sjogren syndrome
A, B	Pharos: P51149	Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease type 2B peripheral neuropathy astrocytic tumor coronary artery disease motor peripheral neuropathy ovarian cancer peripheral nervous system disease attention deficit hyperactivity disorder, inattentive type glioblastoma myocardial ischemia Pain Disorder breast carcinoma chronic kidney disease malignant glioma Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease type 2B peripheral neuropathy astrocytic tumor coronary artery disease motor peripheral neuropathy ovarian cancer peripheral nervous system disease attention deficit hyperactivity disorder, inattentive type glioblastoma myocardial ischemia Pain Disorder breast carcinoma chronic kidney disease malignant glioma neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma

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.