4DCN

Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex 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	d4dcna_	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	d4dcnb_	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	d4dcnc_	All alpha proteins	BAR/IMD domain-like	BAR/IMD domain-like	Arfaptin, Rac-binding fragment	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4dcnd_	All alpha proteins	BAR/IMD domain-like	BAR/IMD domain-like	Arfaptin, Rac-binding fragment	automated matches	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	SCOP2B Superfamily	Ras-like P-loop GTPases	8057422	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057422	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	BAR/IMD domain-like	8033639	3000528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	BAR/IMD domain-like	8033639	3000528	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	PF00025	e4dcnA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00025	ECOD (1.6)
B	PF00025	e4dcnB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00025	ECOD (1.6)
C	PF06456	e4dcnC1	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: BAR/IMD domain-like (From Topology)	T: BAR/IMD domain-like	F: PF06456	ECOD (1.6)
D	PF06456	e4dcnD1	A: alpha duplicates or obligate multimers	X: BAR/IMD domain-like	H: BAR/IMD domain-like (From Topology)	T: BAR/IMD domain-like	F: PF06456	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.1270.60	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
D	1.20.1270.60	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain
C, D	PF06456	Arfaptin-like domain (Arfaptin)	Arfaptin-like domain	Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer o ...	Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer of three-helix coiled-coils [1]. The N-terminal region of ICA69 is similar to arfaptin [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 phospholipase D activator activity phospholipase activator activity lipase activator activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding protein binding binding protein domain specific binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity phospholipase D activator activity 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 organic cyclic compound 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 hydrolase activity, acting on acid anhydrides catalytic activity	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 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 protein localization to Golgi apparatus protein localization to organelle vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi cellular metabolic process 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 cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm Golgi membrane membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm Golgi membrane membrane bounding membrane of organelle organelle membrane cytosol trans-Golgi network membrane
C, D	Arfaptin-2	small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding GTP-dependent protein binding phospholipid binding lipid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding GTP-dependent protein binding phospholipid binding lipid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cell adhesion molecule binding cadherin binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding membrane curvature sensor activity identical protein binding	lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis cellular component assembly lamellipodium organization cellular process cellular component organization or biogenesis cell projection assembly organelle organization actin cytoskeleton organization actin filament-based process lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis cellular component assembly lamellipodium organization cellular process cellular component organization or biogenesis cell projection assembly organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization 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 intracellular protein transport ruffle organization cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette signal transduction regulation of Arp2/3 complex-mediated actin nucleation regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process regulation of actin nucleation regulation of actin filament organization actin filament organization Arp2/3 complex-mediated actin nucleation regulation of organelle organization regulation of actin cytoskeleton organization regulation of supramolecular fiber organization actin nucleation supramolecular fiber organization cellular component disassembly catabolic process macroautophagy cellular metabolic process autophagy cellular catabolic process mitophagy organelle disassembly metabolic process autophagy of mitochondrion process utilizing autophagic mechanism mitochondrion organization autophagosome organization autophagosome assembly organelle assembly vacuole organization protein localization to phagophore assembly site	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cell periphery cell cortex cytoplasm cytosol plasma membrane membrane Golgi apparatus endomembrane system ruffle cell projection cell leading edge plasma membrane bounded cell projection Golgi apparatus subcompartment organelle subcompartment trans-Golgi network membrane trans-Golgi network organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005225	Small GTP-binding protein domain	Domain
A, B	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D	IPR030798	Arfaptin family	Family
C, D	IPR010504	Arfaptin homology (AH) domain	Domain
C, D	IPR027267	AH/BAR domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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
C, D	Pharos: P53365	ductal breast carcinoma in situ invasive ductal breast carcinoma lung cancer

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.