5OSI | pdb_00005osi

Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)

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	d5osia_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	YfcE-like	Vacuolar protein sorting 29, VPS29	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5osid_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	YfcE-like	Vacuolar protein sorting 29, VPS29	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5osij_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	YfcE-like	Vacuolar protein sorting 29, VPS29	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5osig_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	YfcE-like	Vacuolar protein sorting 29, VPS29	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)
H	SCOP2B Superfamily	ARM repeat-like	8051797	3000116	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ARM repeat-like	8051797	3000116	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ARM repeat-like	8051797	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8051797	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8036532	3001067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-dependent phosphatases	8036532	3001067	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Metallo-dependent phosphatases	8036532	3001067	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Metallo-dependent phosphatases	8036532	3001067	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)
H		e5osiH1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
K		e5osiK1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
E		e5osiE1	A: Cryptochrome/photolyase FAD-binding domain-related	X: Cryptochrome/photolyase FAD-binding domain-related	H: Undecaprenyl diphosphate synthase	T: Pkinase, ABC1	F:	ECOD (20:10:01)
B		e5osiB1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
A		e5osiA1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
D		e5osiD1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
J		e5osiJ1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)
G		e5osiG1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: ATP-synt_VA_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.25.40.660	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C	CATH (4.3.0)
K	1.25.40.660	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C	CATH (4.3.0)
E	1.25.40.660	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C	CATH (4.3.0)
B	1.25.40.660	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C	CATH (4.3.0)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
D	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
J	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
G	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF12850	Calcineurin-like phosphoesterase superfamily domain (Metallophos_2)	Calcineurin-like phosphoesterase superfamily domain	Members of this family are part of the Calcineurin-like phosphoesterase superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I	Interaptin	-	-	-
B, E, H, K	Vacuolar protein sorting-associated protein 35	D1 dopamine receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding dopamine receptor binding	regulation of cellular process positive regulation of biological process dopamine metabolic process catechol-containing compound metabolic process regulation of primary metabolic process biogenic amine biosynthetic process positive regulation of metabolic process catecholamine metabolic process positive regulation of biosynthetic process dopamine biosynthetic process catecholamine biosynthetic process catechol-containing compound biosynthetic process positive regulation of amine metabolic process positive regulation of cellular process regulation of cellular process positive regulation of biological process dopamine metabolic process catechol-containing compound metabolic process regulation of primary metabolic process biogenic amine biosynthetic process positive regulation of metabolic process catecholamine metabolic process positive regulation of biosynthetic process dopamine biosynthetic process catecholamine biosynthetic process catechol-containing compound biosynthetic process positive regulation of amine metabolic process positive regulation of cellular process positive regulation of dopamine biosynthetic process regulation of dopamine metabolic process regulation of biosynthetic process regulation of biological process regulation of amine metabolic process biological regulation primary metabolic process regulation of dopamine biosynthetic process positive regulation of dopamine metabolic process amine metabolic process biosynthetic process amine biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process metabolic process cellular process regulation of catecholamine metabolic process regulation of metabolic process biogenic amine metabolic process protein destabilization regulation of protein stability regulation of biological quality catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy process utilizing autophagic mechanism cellular localization transport intracellular transport mitochondrion to lysosome vesicle-mediated transport lysosomal transport establishment of localization vesicle-mediated transport mitochondrion-derived vesicle mediated transport localization establishment of localization in cell vacuolar transport mitochondrial transport regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process vesicle-mediated transport in synapse trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication positive regulation of cell communication regulation of localization establishment of protein localization regulation of protein localization positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport secretion by cell regulation of secretion by cell positive regulation of secretion signal release intracellular protein localization regulation of Wnt protein secretion secretion regulation of transport positive regulation of Wnt protein secretion establishment of protein localization to extracellular region regulation of establishment of protein localization export from cell regulation of protein transport Wnt protein secretion protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization positive regulation of signaling developmental process multicellular organismal process regulation of cellular component organization regulation of developmental process nervous system development developmental maturation synapse maturation cellular component organization regulation of synapse organization multicellular organism development regulation of synapse maturation cell junction organization anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis system development regulation of organelle organization organelle organization regulation of mitochondrion organization mitochondrion organization endosomal transport cytosolic transport retrograde transport, endosome to Golgi regulation of protein catabolic process in the vacuole negative regulation of biological process lysosomal protein catabolic process negative regulation of protein catabolic process in the vacuole macromolecule catabolic process negative regulation of protein catabolic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process protein catabolic process in the vacuole negative regulation of metabolic process protein catabolic process negative regulation of lysosomal protein catabolic process regulation of lysosomal protein catabolic process regulation of protein catabolic process positive regulation of locomotion locomotion involved in locomotory behavior behavior regulation of behavior positive regulation of locomotion involved in locomotory behavior locomotory behavior positive regulation of behavior regulation of locomotion regulation of locomotion involved in locomotory behavior positive regulation of multicellular organismal process regulation of multicellular organismal process locomotion establishment of protein localization to plasma membrane endocytic recycling neurotransmitter receptor transport to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane protein localization to cell periphery neurotransmitter receptor transport establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane protein-containing complex localization vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport intracellular protein transport presynapse organization regulation of terminal button organization terminal button organization regulation of presynapse organization negative regulation of protein localization voluntary musculoskeletal movement multicellular organismal movement musculoskeletal movement system process nervous system process neuromuscular process protein localization to endosome protein localization to organelle regulation of presynapse assembly cellular component biogenesis cellular component assembly cell junction assembly regulation of synapse assembly regulation of cellular component biogenesis regulation of cell junction assembly synapse assembly presynapse assembly regulation of defense response response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response dendritic spine maintenance cell projection organization cellular component maintenance regulation of dendritic spine maintenance plasma membrane bounded cell projection organization dendritic spine organization postsynapse organization regulation of cell projection organization regulation of postsynapse organization neuron projection organization regulation of plasma membrane bounded cell projection organization positive regulation of protein metabolic process positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of protein localization to cell periphery regulation of protein localization to cell periphery lysosome organization vacuole organization lytic vacuole organization mitochondrial fragmentation involved in apoptotic process apoptotic mitochondrial changes apoptotic process cell death programmed cell death regulation of postsynapse assembly postsynapse assembly positive regulation of organelle organization positive regulation of cellular component organization positive regulation of developmental process regulation of anatomical structure morphogenesis organelle fission mitochondrial fission anatomical structure morphogenesis regulation of mitochondrial fission positive regulation of mitochondrial fission negative regulation of protein homooligomerization regulation of protein oligomerization regulation of protein homooligomerization regulation of protein-containing complex assembly protein-containing complex assembly protein homooligomerization negative regulation of protein oligomerization negative regulation of cellular component organization protein-containing complex organization negative regulation of protein-containing complex assembly protein complex oligomerization transcytosis late endosome to lysosome transport negative regulation of transport negative regulation of late endosome to lysosome transport regulation of intracellular transport negative regulation of intracellular transport negative regulation of vacuolar transport regulation of vacuolar transport regulation of cellular localization regulation of late endosome to lysosome transport cellular response to nitrogen compound cellular response to stimulus response to dopamine positive regulation of signal transduction cellular response to dopamine response to monoamine regulation of signal transduction regulation of dopamine receptor signaling pathway positive regulation of response to stimulus response to catecholamine cellular response to catecholamine stimulus signal transduction regulation of G protein-coupled receptor signaling pathway G protein-coupled dopamine receptor signaling pathway response to oxygen-containing compound response to nitrogen compound positive regulation of G protein-coupled receptor signaling pathway cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to monoamine stimulus response to chemical G protein-coupled receptor signaling pathway positive regulation of dopamine receptor signaling pathway cell surface receptor signaling pathway Wnt signaling pathway regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process protein localization to synapse neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane neurotransmitter receptor transport, endosome to postsynaptic membrane protein localization to postsynaptic membrane regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to postsynapse protein localization to cell junction receptor localization to synapse	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol synapse extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol synapse cell junction dopaminergic synapse glutamatergic synapse cell projection neuron projection plasma membrane bounded cell projection vacuolar membrane membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome intracellular vesicle mitochondrion-derived vesicle cytoplasmic vesicle perinuclear region of cytoplasm endosome membrane endosome endomembrane system cytoplasmic vesicle membrane vesicle membrane somatodendritic compartment cell body neuronal cell body protein-containing complex membrane protein complex retromer complex presynapse tubular endosome early endosome retromer, cargo-selective complex postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse late endosome
A, D, G, J	Vacuolar protein sorting-associated protein 29	cation binding ion binding binding metal ion binding small molecule binding	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane membrane protein complex retromer complex retromer, cargo-selective complex cytosol endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E, H, K	IPR016024	Armadillo-type fold	Homologous Superfamily
B, E, H, K	IPR005378	Vacuolar protein sorting-associated protein 35	Family
B, E, H, K	IPR042491	Vacuolar protein sorting-associated protein 35, C-terminal	Homologous Superfamily
A, D, G, J	IPR000979	Phosphodiesterase MJ0936/Vps29	Family
A, D, G, J	IPR024654	Calcineurin-like phosphoesterase domain, lpxH-type	Domain
A, D, G, J	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, D, G, J	IPR028661	Vacuolar protein sorting-associated protein 29	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E, H, K	Pharos: Q96QK1	Parkinson disease Parkinson disease 17 schizophrenia Autosomal dominant late onset Parkinson disease intellectual disability neurodegenerative disease
A, D, G, J	Pharos: Q9UBQ0	breast carcinoma ovarian cancer hereditary spastic paraplegia pancreatic ductal adenocarcinoma malignant pancreatic neoplasm

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.