4EMZ | pdb_00004emz

HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)

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)
E [auth A]	d4emza_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth M]	d4emzm_	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	mu adaptin domain-like	8083652	3000810	SCOP2B (2022-06-29)
F [auth M]	SCOP2B Superfamily	mu adaptin domain-like	8083652	3000810	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 [auth C]	Transgly	e4emzC2	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Transgly	ECOD (develop294)
D [auth B]	Transgly	e4emzB2	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Transgly	ECOD (develop294)
E [auth A]	SpaA	e4emzA3	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SpaA	ECOD (develop294)
F [auth M]	Fer4_13	e4emzM3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Fer4_13	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth C]	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
D [auth B]	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
E [auth A]	2.60.40.1170	Mainly Beta	Sandwich	Immunoglobulin-like	Mu homology domain, subdomain B	CATH (4.3.0)
F [auth M]	2.60.40.1170	Mainly Beta	Sandwich	Immunoglobulin-like	Mu homology domain, subdomain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], C [auth E]	PF06623	MHC_I C-terminus (MHC_I_C)	MHC_I C-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], D [auth B]	Protein Nef	protein binding binding signaling receptor binding thioesterase binding enzyme 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 protein binding binding signaling receptor binding thioesterase binding enzyme 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 SH3 domain binding protein domain specific binding CD4 receptor binding kinase binding protein kinase binding MHC class I protein binding MHC protein binding ATPase 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 cellular component organization cellular component biogenesis cellular component assembly 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 cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein trimerization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis 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 cellular process symbiont-mediated suppression of host autophagy symbiont-mediated perturbation of host autophagy cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process response to stimulus signaling biological regulation regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling intracellular signaling cassette regulation of calcium-mediated signaling regulation of cell communication signal transduction negative regulation of biological process carbohydrate derivative metabolic process regulation of primary metabolic process negative regulation of cellular process protein metabolic process regulation of glycoprotein biosynthetic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process carbohydrate derivative biosynthetic process regulation of biosynthetic process negative regulation of glycoprotein biosynthetic process negative regulation of glycoprotein metabolic process regulation of protein metabolic process negative regulation of metabolic process glycoprotein biosynthetic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process macromolecule biosynthetic process regulation of glycoprotein metabolic process biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of host apoptosis symbiont-mediated perturbation of host programmed cell death symbiont-mediated suppression of host programmed cell death regulation of killing of cells of another organism disruption of cell in another organism regulation of cell killing symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism killing of cells of another organism cell killing	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part extracellular region virion component host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part extracellular region virion component 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
B [auth D], C [auth E]	MHC-I	binding antigen binding peptide antigen binding peptide binding TAP complex binding protein-containing complex binding beta-2-microglobulin binding protein binding signaling receptor binding T cell receptor binding CD8 receptor binding RNA binding nucleic acid binding TAP binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated cytotoxicity T cell mediated immunity response to tumor cell T cell mediated cytotoxicity directed against tumor cell target response to stimulus immune response immune response to tumor cell leukocyte mediated cytotoxicity adaptive immune response response to biotic stimulus immune effector process T cell mediated immune response to tumor cell immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated cytotoxicity T cell mediated immunity response to tumor cell T cell mediated cytotoxicity directed against tumor cell target response to stimulus immune response immune response to tumor cell leukocyte mediated cytotoxicity adaptive immune response response to biotic stimulus immune effector process T cell mediated immune response to tumor cell immune system process leukocyte mediated immunity cellular process cell killing multicellular organismal process regulation of cellular process positive regulation of cell population proliferation CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation regulation of leukocyte activation CD8-positive, alpha-beta T cell proliferation positive regulation of alpha-beta T cell proliferation regulation of cell activation positive regulation of CD8-positive, alpha-beta T cell activation positive regulation of cell activation T cell activation alpha-beta T cell proliferation lymphocyte proliferation positive regulation of leukocyte activation positive regulation of CD8-positive, alpha-beta T cell proliferation alpha-beta T cell activation regulation of immune system process positive regulation of immune system process regulation of leukocyte proliferation regulation of biological process positive regulation of T cell activation cell population proliferation regulation of CD8-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of alpha-beta T cell activation mononuclear cell proliferation regulation of cell population proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of multicellular organismal process positive regulation of biological process positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte proliferation leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation regulation of alpha-beta T cell proliferation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of CD8-positive, alpha-beta T cell activation regulation of lymphocyte activation regulation of immune effector process positive regulation of leukocyte mediated immunity T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of immune response cytokine production positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response regulation of adaptive immune response regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus positive regulation of production of molecular mediator of immune response regulation of immune response metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of response to stimulus regulation of T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of lymphocyte mediated immunity positive regulation of gene expression positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus innate immune response detection of external biotic stimulus detection of biotic stimulus detection of bacterium detection of stimulus detection of other organism antigen processing and presentation antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I negative regulation of biological process negative regulation of lymphocyte mediated immunity negative regulation of natural killer cell mediated immunity natural killer cell mediated immunity regulation of natural killer cell mediated immunity regulation of innate immune response negative regulation of immune response negative regulation of immune effector process negative regulation of response to external stimulus negative regulation of defense response natural killer cell mediated cytotoxicity regulation of cell killing negative regulation of natural killer cell mediated cytotoxicity regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity regulation of response to external stimulus negative regulation of response to biotic stimulus protection from natural killer cell mediated cytotoxicity regulation of response to stress negative regulation of leukocyte mediated cytotoxicity negative regulation of cellular process negative regulation of cell killing negative regulation of response to stimulus regulation of leukocyte mediated cytotoxicity negative regulation of immune system process negative regulation of leukocyte mediated immunity negative regulation of innate immune response positive regulation of memory T cell activation regulation of memory T cell activation memory T cell activation peptide antigen assembly with MHC class I protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class I protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of exogenous peptide antigen via MHC class I antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen positive regulation of leukocyte mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of T cell mediated cytotoxicity positive regulation of cell killing cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway activation of immune response antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent antigen processing and presentation of endogenous peptide antigen via MHC class Ib antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib regulation of type II interferon production type II interferon production positive regulation of type II interferon production defense response to Gram-positive bacterium	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle MHC class I protein complex MHC protein complex protein-containing complex plasma membrane protein complex membrane protein complex intracellular organelle intracellular anatomical structure endoplasmic reticulum exit site endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle Golgi apparatus Golgi membrane MHC class I peptide loading complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Golgi apparatus subcompartment Golgi cisterna Golgi stack Golgi medial cisterna lumenal side of endoplasmic reticulum membrane lumenal side of membrane endosome membrane endosome recycling endosome recycling endosome membrane early endosome early endosome membrane transport vesicle transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle
E [auth A], F [auth M]	AP-1 complex subunit mu-1	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 vesicle organization cellular component organization 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 organization cellular component organization melanosome organization organelle organization pigmentation cellular pigmentation cellular component organization or biogenesis pigment granule organization organelle assembly cellular component biogenesis cellular component assembly melanosome assembly vesicle-mediated transport platelet dense granule organization secretory granule organization endomembrane system organization cellular response to stimulus pigment cell differentiation response to stimulus cellular developmental process developmental pigmentation endosome to pigment granule transport cell differentiation cellular pigment accumulation developmental process endosome to melanosome transport pigment accumulation response to external stimulus developmental maturation pigment granule maturation	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 vacuolar 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 vacuolar membrane membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network clathrin-coated vesicle coated vesicle synapse cell junction cytosol trans-Golgi network membrane protein-containing complex vesicle coat membrane protein complex transport vesicle membrane clathrin coat of trans-Golgi network vesicle membrane coat trans-Golgi network transport vesicle membrane trans-Golgi network transport vesicle AP-type membrane coat adaptor complex AP-1 adaptor complex vesicle membrane clathrin vesicle coat Golgi-associated vesicle clathrin-coated vesicle membrane transport vesicle coated membrane clathrin coat coated vesicle membrane cytoplasmic vesicle membrane Golgi-associated vesicle membrane clathrin adaptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], D [auth B]	IPR001558	HIV negative factor Nef	Family
A [auth C], D [auth B]	IPR027481	HIV-1 Nef protein, core domain superfamily	Homologous Superfamily
A [auth C], D [auth B]	IPR027480	HIV-1 Nef protein, anchor domain superfamily	Homologous Superfamily
B [auth D], C [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth D], C [auth E]	IPR010579	MHC class I, alpha chain, C-terminal	Domain
B [auth D], C [auth E]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B [auth D], C [auth E]	IPR001039	MHC class I alpha chain, alpha1 alpha2 domains	Domain
B [auth D], C [auth E]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth D], C [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth D], C [auth E]	IPR007110	Immunoglobulin-like domain	Domain
B [auth D], C [auth E]	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
B [auth D], C [auth E]	IPR003597	Immunoglobulin C1-set	Domain
B [auth D], C [auth E]	IPR011161	MHC class I-like antigen recognition-like	Domain
B [auth D], C [auth E]	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
E [auth A], F [auth M]	IPR050431	Adaptor complexes medium subunit	Family
E [auth A], F [auth M]	IPR011012	Longin-like domain superfamily	Homologous Superfamily
E [auth A], F [auth M]	IPR022775	AP complex, mu/sigma subunit	Domain
E [auth A], F [auth M]	IPR036168	AP-2 complex subunit mu, C-terminal superfamily	Homologous Superfamily
E [auth A], F [auth M]	IPR028565	Mu homology domain	Domain
E [auth A], F [auth M]	IPR018240	Clathrin adaptor, mu subunit, conserved site	Conserved Site
E [auth A], F [auth M]	IPR001392	Clathrin adaptor, mu subunit	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D], C [auth E]	Pharos: P04439	malignant glioma parapsoriasis plasma cell myeloma Stevens-Johnson syndrome thrombocytopenia ankylosing spondylitis mixed glioma juvenile idiopathic arthritis birdshot chorioretinopathy Drug-Induced Acute Liver Injury pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia paranoid schizophrenia glioma pilocytic astrocytoma malignant glioma parapsoriasis plasma cell myeloma Stevens-Johnson syndrome thrombocytopenia ankylosing spondylitis mixed glioma juvenile idiopathic arthritis birdshot chorioretinopathy Drug-Induced Acute Liver Injury pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia paranoid schizophrenia glioma pilocytic astrocytoma prostate carcinoma allergic rhinitis herpes zoster schizophrenia autism juvenile dermatomyositis autoimmune disease lung adenocarcinoma toxic epidermal necrolysis breast cancer malignant ependymoma cutaneous lupus erythematosus nasopharyngeal disease pancreatic intraductal papillary-mucinous carcinoma Duchenne muscular dystrophy Graves disease psoriatic arthritis alopecia IgA glomerulonephritis squamous cell lung carcinoma astrocytic tumor autism spectrum disorder subependymal giant cell astrocytoma bipolar disorder lung cancer cancer dermatomyositis ovarian cancer drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm endogenous depression glioblastoma head and neck squamous cell carcinoma plasma cell neoplasm hepatocellular carcinoma rheumatoid arthritis alopecia areata attention deficit hyperactivity disorder, inattentive type inherited disease susceptibility liver disease lung carcinoma vitiligo cervical cancer colorectal cancer myeloid neoplasm