Annotations: 2NEF

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2nefa_	Alpha and beta proteins (a+b)	Regulatory factor Nef	Regulatory factor Nef	Regulatory factor Nef	Regulatory factor Nef	(Human immunodeficiency virus type 1 BH10 ) [TaxId: 11678 ],	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	8023500	4001772	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Regulatory factor Nef	8035880	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	F-protein	e2nefA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	NEGATIVE FACTOR (F-PROTEIN)	SH3 domain binding protein binding binding protein domain specific binding signaling receptor binding CD4 receptor binding kinase binding enzyme binding protein kinase binding thioesterase binding MHC class I protein binding MHC protein binding guanyl nucleotide binding GTP binding SH3 domain binding protein binding binding protein domain specific binding signaling receptor binding CD4 receptor binding kinase binding enzyme binding protein kinase binding thioesterase binding MHC class I protein binding MHC protein 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 ATPase binding	viral process viral life cycle regulation of CD4 production regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process carbohydrate derivative metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process protein metabolic process viral process viral life cycle regulation of CD4 production regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process carbohydrate derivative metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process organic substance metabolic process organic substance biosynthetic 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 biological process organonitrogen compound metabolic process negative regulation of CD4 production cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process biological regulation glycoprotein biosynthetic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of glycoprotein metabolic process regulation of cellular biosynthetic process biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process CD4 biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus regulation of signaling response to stimulus signaling 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 symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms 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 modulation by virus of host process virus-mediated perturbation of host defense response perturbation by virus of host immune response modulation by virus of host cellular process suppression by virus of host autophagy modulation by virus of host autophagy symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II symbiont-mediated suppression of host T-cell mediated immune response	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	IPR001558	HIV negative factor Nef	Family
A	IPR027480	HIV-1 Nef protein, anchor domain superfamily	Homologous Superfamily
A	IPR027481	HIV-1 Nef protein, core domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	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.