4NEE | pdb_00004nee

crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L [auth C]	d4neec1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
L [auth C]	d4neec2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
K	d4neek1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
K	d4neek2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
J [auth H]	d4neeh1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
J [auth H]	d4neeh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
I [auth E]	d4neee1	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
I [auth E]	d4neee2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
D [auth I]	d4neei_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth F]	d4neef_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B [auth L]	d4neel_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A [auth D]	d4need_	Alpha and beta proteins (a+b)	Profilin-like	SNARE-like	Clathrin coat assembly domain	Sigma2 adaptin (clathrin coat assembly protein AP17)	brown rat,rat,rats (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth C]	SCOP2 Family	Regulatory factor Nef	8086599	4001772	SCOP2 (2022-06-29)
L [auth C]	SCOP2 Superfamily	Regulatory factor Nef	8086600	3000353	SCOP2 (2022-06-29)
K	SCOP2B Superfamily	Regulatory factor Nef	8086600	3000353	SCOP2B (2022-06-29)
J [auth H]	SCOP2B Superfamily	Regulatory factor Nef	8086600	3000353	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Regulatory factor Nef	8086600	3000353	SCOP2B (2022-06-29)
D [auth I]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	SNARE-like	8093628	3001113	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)
L [auth C]	Acetyltransf_1	e4neeC3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acetyltransf_1	ECOD (v294.1)
I [auth E]	Acetyltransf_1	e4neeE3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acetyltransf_1	ECOD (v294.1)
H [auth A]	KAsynt_C_assoc	e4neeA1	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (v294.1)
G [auth J]		e4neeJ1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F:	ECOD (v294.1)
F [auth B]	Hexapep	e4neeB1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Hexapep	ECOD (v294.1)
E [auth G]	Gtf3_C	e4neeG1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Gtf3_C	ECOD (v294.1)
D [auth I]		e4neeI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F:	ECOD (v294.1)
C [auth F]		e4neeF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F:	ECOD (v294.1)
B [auth L]		e4neeL1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F:	ECOD (v294.1)
A [auth D]	PolyA_pol	e4neeD1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: PolyA_pol	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth C]	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
K	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
J [auth H]	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
I [auth E]	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
H [auth A]	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
G [auth J]	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
F [auth B]	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
E [auth G]	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
D [auth I]	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
C [auth F]	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
B [auth L]	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
A [auth D]	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth G], F [auth B], G [auth J], H [auth A]	PF01602	Adaptin N terminal region (Adaptin_N)	Adaptin N terminal region	-	Repeat
A [auth D], B [auth L], C [auth F], D [auth I]	PF01217	Clathrin adaptor complex small chain (Clat_adaptor_s)	Clathrin adaptor complex small chain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth E], J [auth H], K, L [auth C]	Protein Nef	SH3 domain binding protein binding binding protein domain specific 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 SH3 domain binding protein binding binding protein domain specific 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	symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I symbiont-mediated suppression of host antigen processing and presentation modulation of process of another organism symbiont-mediated suppression of host adaptive immune response viral process viral life cycle symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I symbiont-mediated suppression of host antigen processing and presentation modulation of process of another organism symbiont-mediated suppression of host adaptive immune response viral process viral life cycle symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of metabolic process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host autophagy symbiont-mediated perturbation of host autophagy	cellular anatomical structure membrane extracellular region virion component host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm cellular anatomical structure membrane extracellular region virion component host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm host cell endomembrane system host intracellular region
E [auth G], F [auth B], G [auth J], H [auth A]	AP-2 complex subunit alpha-2	binding phospholipid binding lipid binding phosphatidylinositol binding protein binding protein domain specific binding kinase binding enzyme binding protein serine/threonine kinase binding protein kinase binding protein-containing complex binding cargo adaptor activity protein-macromolecule adaptor activity molecular adaptor activity binding phospholipid binding lipid binding phosphatidylinositol binding protein binding protein domain specific binding kinase binding enzyme binding protein serine/threonine kinase binding protein kinase binding protein-containing complex binding cargo adaptor activity protein-macromolecule adaptor activity molecular adaptor activity clathrin-cargo adaptor activity disordered domain specific binding	synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis clathrin-dependent endocytosis receptor-mediated endocytosis establishment of protein localization intracellular transport protein transport macromolecule localization intracellular protein localization intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system intracellular organelle membrane coat bounding membrane of organelle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system intracellular organelle membrane coat bounding membrane of organelle AP-type membrane coat adaptor complex AP-2 adaptor complex cytoplasmic vesicle vesicle membrane clathrin-coated pit clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex intracellular membrane-bounded organelle coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane clathrin adaptor complex synapse cell junction transport vesicle presynapse synaptic vesicle secretory vesicle exocytic vesicle
A [auth D], B [auth L], C [auth F], D [auth I]	AP-2 complex subunit sigma	cargo adaptor activity protein-macromolecule adaptor activity molecular adaptor activity clathrin-cargo adaptor activity	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 synaptic vesicle endocytosis import into cell 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 synaptic vesicle endocytosis import into cell synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling endocytosis clathrin-dependent endocytosis receptor-mediated endocytosis receptor internalization postsynaptic neurotransmitter receptor internalization biological regulation neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis regulation of biological quality	cellular anatomical structure synapse cell junction cell periphery plasma membrane membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system intracellular organelle cellular anatomical structure synapse cell junction cell periphery plasma membrane membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system intracellular organelle membrane coat bounding membrane of organelle AP-type membrane coat adaptor complex AP-2 adaptor complex cytoplasmic vesicle vesicle membrane clathrin-coated pit clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex intracellular membrane-bounded organelle coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane clathrin adaptor complex postsynapse transport vesicle presynapse synaptic vesicle secretory vesicle exocytic vesicle glutamatergic synapse extrinsic component of plasma membrane presynaptic endocytic zone presynaptic membrane extrinsic component of presynaptic endocytic zone membrane synaptic membrane extrinsic component of synaptic membrane presynaptic endocytic zone membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth E], J [auth H], K, L [auth C]	IPR001558	HIV negative factor Nef	Family
I [auth E], J [auth H], K, L [auth C]	IPR027480	HIV-1 Nef protein, anchor domain superfamily	Homologous Superfamily
I [auth E], J [auth H], K, L [auth C]	IPR027481	HIV-1 Nef protein, core domain superfamily	Homologous Superfamily
E [auth G], F [auth B], G [auth J], H [auth A]	IPR016024	Armadillo-type fold	Homologous Superfamily
E [auth G], F [auth B], G [auth J], H [auth A]	IPR003164	Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain	Domain
E [auth G], F [auth B], G [auth J], H [auth A]	IPR011989	Armadillo-like helical	Homologous Superfamily
E [auth G], F [auth B], G [auth J], H [auth A]	IPR012295	TBP domain superfamily	Homologous Superfamily
E [auth G], F [auth B], G [auth J], H [auth A]	IPR002553	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Domain
E [auth G], F [auth B], G [auth J], H [auth A]	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
E [auth G], F [auth B], G [auth J], H [auth A]	IPR050840	Adaptor Complexes Large Subunit	Family
E [auth G], F [auth B], G [auth J], H [auth A]	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
E [auth G], F [auth B], G [auth J], H [auth A]	IPR017104	Adaptor protein complex AP-2, alpha subunit	Family
E [auth G], F [auth B], G [auth J], H [auth A]	IPR009028	Coatomer/calthrin adaptor appendage, C-terminal subdomain	Homologous Superfamily
A [auth D], B [auth L], C [auth F], D [auth I]	IPR016635	Adaptor protein complex, sigma subunit	Family
A [auth D], B [auth L], C [auth F], D [auth I]	IPR011012	Longin-like domain superfamily	Homologous Superfamily
A [auth D], B [auth L], C [auth F], D [auth I]	IPR000804	Clathrin adaptor complex, small chain	Conserved Site
A [auth D], B [auth L], C [auth F], D [auth I]	IPR022775	AP complex, mu/sigma subunit	Domain
A [auth D], B [auth L], C [auth F], D [auth I]	IPR027156	AP-2 complex subunit sigma	Family

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.