4NEE

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
D [auth I]	SCOP2B Superfamily	SNARE-like	8093628	3001113	SCOP2B (2022-06-29)
I [auth E]	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)
K	SCOP2B Superfamily	Regulatory factor Nef	8086600	3000353	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth D]	Clat_adaptor_s	e4neeD1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
B [auth L]	Clat_adaptor_s	e4neeL1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
C [auth F]	Clat_adaptor_s	e4neeF1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
D [auth I]	Clat_adaptor_s	e4neeI1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
E [auth G]	Adaptin_N	e4neeG1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
F [auth B]	Adaptin_N	e4neeB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
G [auth J]	Adaptin_N	e4neeJ1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
H [auth A]	Adaptin_N	e4neeA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
I [auth E]	F-protein	e4neeE3	A: a+b three layers	X: Regulatory factor Nef (From Topology)	H: Regulatory factor Nef (From Topology)	T: Regulatory factor Nef	F: F-protein	ECOD (1.6)
J [auth H]	F-protein	e4neeH3	A: a+b three layers	X: Regulatory factor Nef (From Topology)	H: Regulatory factor Nef (From Topology)	T: Regulatory factor Nef	F: F-protein	ECOD (1.6)
K	F-protein	e4neeK2	A: a+b three layers	X: Regulatory factor Nef (From Topology)	H: Regulatory factor Nef (From Topology)	T: Regulatory factor Nef	F: F-protein	ECOD (1.6)
L [auth C]	F-protein	e4neeC3	A: a+b three layers	X: Regulatory factor Nef (From Topology)	H: Regulatory factor Nef (From Topology)	T: Regulatory factor Nef	F: F-protein	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
E [auth G], F [auth B], G [auth J], H [auth A]	PF01602	Adaptin N terminal region (Adaptin_N)	Adaptin N terminal region	-	Repeat
I [auth E], J [auth H], K, L [auth C]	PF00469	Negative factor, (F-Protein) or Nef (F-protein)	Negative factor, (F-Protein) or Nef	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth L], C [auth F], D [auth I]	AP-2 complex subunit sigma	cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity molecular adaptor 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 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 protein-containing complex localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis regulation of biological quality	synapse cell junction cellular anatomical entity cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle synapse cell junction cellular anatomical entity cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle membrane protein complex endomembrane system 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 coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane cytoplasm organelle membrane clathrin adaptor complex postsynapse 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 presynapse presynaptic endocytic zone membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane
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 kinase binding enzyme binding protein domain specific binding protein serine/threonine kinase binding protein kinase binding protein-containing complex binding cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity binding phospholipid binding lipid binding phosphatidylinositol binding protein binding kinase binding enzyme binding protein domain specific binding protein serine/threonine kinase binding protein kinase binding protein-containing complex binding cargo adaptor activity clathrin adaptor activity protein-macromolecule adaptor activity molecular adaptor activity disordered domain specific binding	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 import into cell clathrin-dependent endocytosis receptor-mediated endocytosis endocytosis vesicle-mediated transport	membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle cell periphery plasma membrane membrane protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle cell periphery plasma membrane membrane protein-containing complex vesicle coat membrane protein complex endomembrane system membrane coat bounding membrane of organelle AP-type membrane coat adaptor complex AP-2 adaptor complex vesicle membrane clathrin-coated pit clathrin-coated vesicle endocytic vesicle membrane coated vesicle clathrin vesicle coat 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 coated membrane clathrin-coated endocytic vesicle clathrin coat cytoplasmic vesicle membrane coated vesicle membrane organelle membrane clathrin adaptor complex transport vesicle synapse presynapse synaptic vesicle cell junction secretory vesicle exocytic vesicle
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 organic cyclic compound binding purine nucleotide 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 organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response modulation by symbiont of host process response to host immune response symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response modulation by symbiont of host process response to host immune response 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 response to host response to external biotic stimulus modulation of process of another organism symbiont-mediated suppression of host adaptive immune response suppression by virus of host autophagy modulation by virus of host autophagy viral process modulation by virus of host process modulation by virus of host cellular process symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II	membrane cellular anatomical entity extracellular region virion component host cell plasma membrane host cellular component host cell part host cell membrane host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm host cell endomembrane system membrane cellular anatomical entity extracellular region virion component host cell plasma membrane host cellular component host cell part host cell membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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]	IPR002553	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Domain
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]	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
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]	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
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]	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
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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.