1UPT | pdb_00001upt

Structure of a complex of the golgin-245 GRIP domain with Arl1

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	d1upta_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	ADP-ribosylation factor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1uptc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	ADP-ribosylation factor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1upte_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	ADP-ribosylation factor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1uptg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	ADP-ribosylation factor	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1uptb_	All alpha proteins	GRIP domain	GRIP domain	GRIP domain	Golgi autoantigen, golgin-245	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1uptd_	All alpha proteins	GRIP domain	GRIP domain	GRIP domain	Golgi autoantigen, golgin-245	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1uptf_	All alpha proteins	GRIP domain	GRIP domain	GRIP domain	Golgi autoantigen, golgin-245	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1upth_	All alpha proteins	GRIP domain	GRIP domain	GRIP domain	Golgi autoantigen, golgin-245	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	SCOP2 Family	Ras-like monodomain GTPases	8057421	4004043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8057422	3002022	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057422	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057422	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8057422	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GRIP domain	8041963	3001046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GRIP domain	8041963	3001046	SCOP2B (2022-06-29)
F	SCOP2 Family	GRIP domain	8029584	4000685	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	GRIP domain	8041963	3001046	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	GRIP domain	8041963	3001046	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	Ras	e1uptA1	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)
C	Ras	e1uptC1	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)
E	Ras	e1uptE1	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)
G	Ras	e1uptG1	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)
B	GRIP	e1uptB1	A: alpha duplicates or obligate multimers	X: GRIP domain (From Topology)	H: GRIP domain (From Topology)	T: GRIP domain	F: GRIP	ECOD (1.6)
D	GRIP	e1uptD1	A: alpha duplicates or obligate multimers	X: GRIP domain (From Topology)	H: GRIP domain (From Topology)	T: GRIP domain	F: GRIP	ECOD (1.6)
F	GRIP	e1uptF1	A: alpha duplicates or obligate multimers	X: GRIP domain (From Topology)	H: GRIP domain (From Topology)	T: GRIP domain	F: GRIP	ECOD (1.6)
H	GRIP	e1uptH1	A: alpha duplicates or obligate multimers	X: GRIP domain (From Topology)	H: GRIP domain (From Topology)	T: GRIP domain	F: GRIP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.220.60	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
D	1.10.220.60	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
F	1.10.220.60	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
H	1.10.220.60	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain
B, D, F, H	PF01465	GRIP domain (GRIP)	GRIP domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1	protein binding binding protein domain specific binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity catalytic activity phosphoric ester hydrolase activity phospholipase D activator activity phosphoric diester hydrolase activity hydrolase activity phospholipase activity lipase activity protein binding binding protein domain specific binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity catalytic activity phosphoric ester hydrolase activity phospholipase D activator activity phosphoric diester hydrolase activity hydrolase activity phospholipase activity lipase activity phospholipase D activity hydrolase activity, acting on ester bonds phospholipase activator activity lipase activator activity 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 cation binding metal ion binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization to Golgi apparatus protein localization to organelle vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi metabolic process toxin metabolic process secondary metabolic process cellular component organization organelle organization cellular component organization or biogenesis Golgi organization endomembrane system organization	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm Golgi membrane membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm Golgi membrane membrane bounding membrane of organelle organelle membrane cytosol trans-Golgi network membrane
B, D, F, H	GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4	small GTPase binding protein binding binding enzyme binding GTPase binding	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport axon extension multicellular organismal process positive regulation of nervous system development regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth system development developmental process regulation of biological process regulation of cell projection organization positive regulation of cell development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell growth cell morphogenesis cellular component organization regulation of axon extension regulation of nervous system development neurogenesis regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axon extension cellular component organization or biogenesis positive regulation of cellular process positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth biological regulation growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm Golgi membrane membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm Golgi membrane membrane bounding membrane of organelle organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR005225	Small GTP-binding domain	Domain
A, C, E, G	IPR024156	Small GTPase superfamily, ARF type	Family
A, C, E, G	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
A, C, E, G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F, H	IPR000237	GRIP domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: P40616	astrocytic tumor glioblastoma large cell medulloblastoma ovarian cancer Crohn disease hereditary spastic paraplegia medulloblastoma pancreatic ductal adenocarcinoma dermatomyositis invasive ductal breast carcinoma osteosarcoma
B, D, F, H	Pharos: Q13439	Arsenic Poisoning prostate cancer acute myeloid leukemia breast cancer osteosarcoma Becker muscular dystrophy hereditary spastic paraplegia ovarian cancer skin disease

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.