3IK5

SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80)

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
Membrane Protein Annotation: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ik5a_	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	SIV-cpz (Simian immunodeficiency virus - cpz ) [TaxId: 388909 ],	SCOPe (2.08)
B [auth C]	d3ik5c_	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	automated matches	automated matches	SIV-cpz (Simian immunodeficiency virus - cpz ) [TaxId: 388909 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Regulatory factor Nef	8086605	4001772	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Regulatory factor Nef	8086606	3000353	SCOP2 (2022-06-29)
B [auth C]	SCOP2B Superfamily	Regulatory factor Nef	8086606	3000353	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	F-protein	e3ik5A2	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)
B [auth C]	F-protein	e3ik5C2	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	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (4.3.0)
B [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, B [auth C]	PF00469	Negative factor, (F-Protein) or Nef (F-protein)	Negative factor, (F-Protein) or Nef	-	Family
C [auth D], D [auth B]	PF02189	Immunoreceptor tyrosine-based activation motif (ITAM)	Immunoreceptor tyrosine-based activation motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	Protein Nef	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 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 response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction modulation by symbiont of host process viral process 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 response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction modulation by symbiont of host process viral process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process	membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane
C [auth D], D [auth B]	T-cell surface glycoprotein CD3 zeta chain	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity protein heterodimerization activity protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation signal transduction cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of biological process positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response Fc receptor signaling pathway Fc-gamma receptor signaling pathway protein localization regulation of localization cellular localization regulation of protein localization positive regulation of protein localization to cell surface localization protein localization to cell surface regulation of cellular localization cellular macromolecule localization macromolecule localization positive regulation of protein localization regulation of protein localization to cell surface positive regulation of cellular process multicellular organismal process gamma-delta T cell activation T cell activation cell activation lymphocyte activation leukocyte activation alpha-beta T cell activation	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cellular anatomical entity receptor complex cell periphery plasma membrane signaling receptor complex T cell receptor complex Fc-gamma receptor III complex Fc receptor complex membrane-bounded organelle protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cellular anatomical entity receptor complex cell periphery plasma membrane signaling receptor complex T cell receptor complex Fc-gamma receptor III complex Fc receptor complex membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system alpha-beta T cell receptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR001558	HIV negative factor Nef	Family
A, B [auth C]	IPR027481	HIV-1 Nef protein, core domain superfamily	Homologous Superfamily
C [auth D], D [auth B]	IPR024128	T-cell surface glycoprotein CD3 zeta subunit	Family
C [auth D], D [auth B]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
C [auth D], D [auth B]	IPR021663	T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D], D [auth B]	Pharos: P20963	systemic sclerosis immunodeficiency 25 oligoarticular juvenile idiopathic arthritis allergic rhinitis cutaneous lupus erythematosus hematologic disease interstitial cystitis lung carcinoma osteosarcoma Systemic Scleroderma asthma diffuse scleroderma hypothyroidism juvenile idiopathic arthritis lymphatic system disease systemic sclerosis immunodeficiency 25 oligoarticular juvenile idiopathic arthritis allergic rhinitis cutaneous lupus erythematosus hematologic disease interstitial cystitis lung carcinoma osteosarcoma Systemic Scleroderma asthma diffuse scleroderma hypothyroidism juvenile idiopathic arthritis lymphatic system disease psoriasis cancer Hashimoto thyroiditis lung cancer rheumatoid factor-negative juvenile idiopathic arthritis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth C], C [auth D], D [auth B]	OPM				Negative factor (Nef) protein

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.