P04601 (NEF_HV1H2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein Nef

Alternative name(s):
3'ORF
Negative factor
Short name=F-protein

Cleaved into the following chain:

1. C-terminal core protein

Gene names

Name:

nef

Organism

Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) [Reference proteome]

Taxonomic identifier

11706 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Primate lentivirus group › Human immunodeficiency virus 1 › HIV-1 group M › HIV-1 M:B

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	206 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Factor of infectivity and pathogenicity, required for optimal virus replication. Alters numerous pathways of T-lymphocytes function and down-regulates immunity surface molecules in order to evade host defense and increase viral infectivity. Alters the functionality of other immunity cells, like dendritic cells, monocytes/macrophages and NK cells. One of the earliest and most abundantly expressed viral proteins. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.12 Ref.14 Ref.15 In infected CD4+ T-lymphocytes, down-regulates the surface MHC-I, mature MHC-II, CD4, CD28, CCR5 and CXCR4 molecules. Mediates internalization and degradation of host CD4 through the interaction of with the cytoplasmic tail of CD4, the recruitment of AP-2 (clathrin adapter protein complex 2), internalization through clathrin coated pits, and subsequent transport to endosomes and lysosomes for degradation. Diverts host MHC-I molecules to the trans-Golgi network-associated endosomal compartments by an endocytic pathway to finally target them for degradation. MHC-I down-regulation may involve AP-1 (clathrin adapter protein complex 1) or possibly Src family kinase-ZAP70/Syk-PI3K cascade recruited by PACS2. In consequence infected cells are masked for immune recognition by cytotoxic T-lymphocytes. Decreasing the number of immune receptors also prevents reinfection by more HIV particles (superinfection). Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.12 Ref.14 Ref.15 Bypasses host T-cell signaling by inducing a transcriptional program nearly identical to that of anti-CD3 cell activation. Interaction with TCR-zeta chain up-regulates the Fas ligand (FasL). Increasing surface FasL molecules and decreasing surface MHC-I molecules on infected CD4+ cells send attacking cytotoxic CD8+ T-lymphocytes into apoptosis By similarity. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.12 Ref.14 Ref.15 Plays a role in optimizing the host cell environment for viral replication without causing cell death by apoptosis. Protects the infected cells from apoptosis in order to keep them alive until the next virus generation is ready to strike. Inhibits the Fas and TNFR-mediated death signals by blocking MAP3K5. Interacts and decreases the half-life of p53, protecting the infected cell against p53-mediated apoptosis. Inhibits the apoptotic signals regulated by the Bcl-2 family proteins through the formation of a Nef/PI3-kinase/PAK2 complex that leads to activation of PAK2 and induces phosphorylation of Bad By similarity. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.12 Ref.14 Ref.15 Extracellular Nef protein targets CD4+ T-lymphocytes for apoptosis by interacting with CXCR4 surface receptors. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.12 Ref.14 Ref.15
Subunit structure	Homodimer By similarity. Interacts with Nef associated p21-activated kinase (PAK2); this interaction activates PAK2. Associates with the Nef-MHC-I-AP1 complex; this complex is required for MHC-I internalization. Interacts (via C-terminus) with host PI3-kinase (via C-terminus). Interacts with host PACS1; this interaction seems to be weak. Interacts with host PACS2. Interacts with host LCK and MAPK3; these interactions inhibit the kinase activity of the latters. Interacts with host ATP6V1H; this interaction may play a role in CD4 endocytosis. Associates with the CD4-Nef-AP2 complex; this complex is required for CD4 internalization. Interacts with TCR-zeta chain; this interaction up-regulates the Fas ligand (FasL) surface expression. Interacts with various cellular proteins including MAP3K5, beta-COP, HCK, and PTE1. Interacts with human GNB2L1/RACK1; this increases Nef phosphorylation by PKC By similarity. Ref.6 Ref.9 Ref.10 Ref.11 Ref.12 Ref.15
Subcellular location	Host cell membrane; Lipid-anchor; Cytoplasmic side By similarity. Host cytoplasm › host perinuclear region By similarity. Virion By similarity. Secreted. Note: Predominantly found in the paranuclear area, probably in the TGN. Correct localization requires PACS1. Also associates with the inner plasma membrane through its N-terminal domain. Nef stimulates its own export via the release of exosomes. Also incorporated in virions at a rate of about 10 molecules per virion, where it is cleaved By similarity. Ref.6 Ref.14
Domain	The N-terminal domain is composed of the N-myristoyl glycine and of a cluster of positively charged amino acids. It is required for inner plasma membrane targeting of Nef and virion incorporation, and thereby for infectivity. This domain is also involved in binding to p53 By similarity. The SH3-binding domain constituted of PxxP motifs mediates binding to several Src family proteins thereby regulating their tyrosine kinase activity. The same motifs also mediates the association with MAPK3, PI3-kinase and TCR-zeta By similarity. The di-leucine internalization motif and a diacidic motif seem to be required for binding to AP-2. The acidic region may play a stabilizing role in the formation of a ternary complex between Nef, the MHC-I cytoplasmic domain, and AP1M1.
Post-translational modification	The virion-associated Nef proteins are cleaved by the viral protease to release the soluble C-terminal core protein. Nef is probably cleaved concomitantly with viral structural proteins on maturation of virus particles By similarity. Ref.13 Phosphorylated on serine residues, probably by host PKC By similarity.
Miscellaneous	HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).
Sequence similarities	Belongs to the lentivirus primate group Nef protein family.
Sequence caution	The sequence AAB50263.1 differs from that shown. Reason: Readthrough of a premature stop codon in position 123 that truncates the Nef protein. The sequence displayed is that of wild-type full-length HXB2-R7 clone. The sequence AAC82597.1 differs from that shown. Reason: Readthrough of a premature stop codon in position 123 that truncates the Nef protein. The sequence displayed is that of wild-type full-length HXB2-R7 clone. The sequence CAA26946.1 differs from that shown. Reason: Readthrough of a premature stop codon in position 123 that truncates the Nef protein. The sequence displayed is that of wild-type full-length HXB2-R7 clone.

Ontologies

Keywords
Biological process	Apoptosis Host-virus interaction Inhibition of host MHC class I molecule presentation by virus Inhibition of host MHC class II molecule presentation by virus Inhibition of host adaptive immune response by virus Inhibition of host autophagy by virus Viral immunoevasion Virulence
Cellular component	Host cell membrane Host cytoplasm Host membrane Membrane Secreted Virion
Developmental stage	Early protein
Disease	AIDS
Domain	SH3-binding
PTM	Lipoprotein Myristate Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	apoptotic process Inferred from electronic annotation. Source: UniProtKB-KW pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW regulation of defense response to virus by virus Traceable author statement. Source: Reactome suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host autophagy Inferred from electronic annotation. Source: UniProtKB-KW viral reproduction Traceable author statement. Source: Reactome
Cellular_component	cytosol Traceable author statement. Source: Reactome host cell perinuclear region of cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from electronic annotation. Source: UniProtKB-KW virion Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	GTP binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ACOT8	O14734	5	EBI-6164028,EBI-1237371	From a different organism.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed; by host By similarity
	Chain	2 – 206	205	Protein Nef		PRO_0000038365
	Chain	58 – 206	149	C-terminal core protein By similarity		PRO_0000038366
Regions
	Region	2 – 57	56	N-terminal; associates with the host plasma membrane By similarity
	Region	7 – 26	20	Necessary for MHC-I internalization Probable
	Region	62 – 65	4	Acidic; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalization and interaction with host PACS1 and PACS2 Probable
	Region	69 – 78	10	SH3-binding; interaction with Src family tyrosine kinases By similarity
	Region	108 – 124	17	Mediates dimerization, Nef-PTE1 interaction By similarity
	Region	148 – 180	33	Binding to ATP6V1H By similarity
	Motif	72 – 75	4	PxxP; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalization Probable
	Motif	164 – 165	2	Di-leucine internalization motif; necessary for CD4 internalization Probable
	Motif	174 – 175	2	Diacidic; necessary for CD4 internalization Probable
	Compositional bias	62 – 65	4	Poly-Glu
Sites
	Site	20	1	Might play a role in AP-1 recruitment to the Nef-MHC-I complex
	Site	57 – 58	2	Cleavage; by viral protease By similarity
Amino acid modifications
	Lipidation	2	1	N-myristoyl glycine; by host By similarity
Experimental info
	Mutagenesis	20	1	M → A: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is internalized but not sequestred in TGN. Ref.8
	Mutagenesis	62 – 65	4	EEEE → AAAA: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is not internalized. Reduced interaction with host PACS1 and PACS2. Ref.10 Ref.11
	Mutagenesis	62 – 65	4	EEEE → AAEA: About 50% loss of Nef-induced MHC-I down-regulation. Ref.10 Ref.11
	Mutagenesis	62 – 65	4	EEEE → AEAA: About 50% loss of Nef-induced MHC-I down-regulation. Ref.10 Ref.11
	Mutagenesis	62 – 65	4	EEEE → DDDD: No effect on Nef-induced MHC-I down-regulation. Ref.10 Ref.11
	Mutagenesis	62 – 64	3	EEE → AAA: About 50% loss of Nef-induced MHC-I down-regulation.
	Mutagenesis	62 – 63	2	EE → AA: Almost no effect on Nef-induced MHC-I down-regulation.
	Mutagenesis	63 – 65	3	EEE → AAA: About 50% loss of Nef-induced MHC-I down-regulation. Ref.8
	Mutagenesis	63 – 64	2	EE → AA: Almost no effect on Nef-induced MHC-I down-regulation.
	Mutagenesis	64 – 65	2	EE → AA: Almost no effect on Nef-induced MHC-I down-regulation.
	Mutagenesis	72	1	P → A: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is not internalized; when associated with A-75. Ref.8
	Mutagenesis	75	1	P → A: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is not internalized; when associated with A-72. Ref.8
	Mutagenesis	123	1	D → E: Complete loss of Nef-induced MHC-I down-regulation, CD4 down-regulation, and enhancement of infectivity. Activates PAK2 twofold over wild-type levels.
	Sequence conflict	29	1	R → G in CAA26946. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P04601 [UniParc]. Last modified February 9, 2010. Version 5. Checksum: 5A26976E95483E9C	FASTA	206	23,469
	10 20 30 40 50 60 MGGKWSKSSV IGWPTVRERM RRAEPAADRV GAASRDLEKH GAITSSNTAA TNAACAWLEA 70 80 90 100 110 120 QEEEEVGFPV TPQVPLRPMT YKAAVDLSHF LKEKGGLEGL IHSQRRQDIL DLWIYHTQGY 130 140 150 160 170 180 FPDWQNYTPG PGVRYPLTFG WCYKLVPVEP DKIEEANKGE NTSLLHPVSL HGMDDPEREV 190 200 LEWRFDSRLA FHHVARELHP EYFKNC

References

[1]	"Polymorphism of the 3' open reading frame of the virus associated with the acquired immune deficiency syndrome, human T-lymphotropic virus type III." Ratner L., Starcich B.R., Josephs S.F., Hahn B.H., Reddy E.P., Livak K.J., Petteway S.R. Jr., Pearson M.L., Haseltine W.A., Arya S.K., Wong-staal F. Nucleic Acids Res. 13:8219-8229(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Complete nucleotide sequences of functional clones of the AIDS virus." Ratner L., Fisher A., Jagodzinski L.L., Mitsuya H., Liou R.-S., Gallo R.C., Wong-Staal F. AIDS Res. Hum. Retroviruses 3:57-69(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	Ratner L., Fisher A., Jagodzinski L.L., Mitsuya H., Liou R.-S., Gallo R.C., Wong-Staal F. Submitted (APR-1997) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[4]	"Nef induces CD4 endocytosis: requirement for a critical dileucine motif in the membrane-proximal CD4 cytoplasmic domain." Aiken C., Konner J., Landau N.R., Lenburg M.E., Trono D. Cell 76:853-864(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: Isolate HXB2-R7.
[5]	"Nef-induced CD4 and major histocompatibility complex class I (MHC-I) down-regulation are governed by distinct determinants: N-terminal alpha helix and proline repeat of Nef selectively regulate MHC-I trafficking." Mangasarian A., Piguet V., Wang J.-K., Chen Y.-L., Trono D. J. Virol. 73:1964-1973(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: Isolate HXB2-R7.
[6]	"HIV-1 Nef protein binds to the cellular protein PACS-1 to downregulate class I major histocompatibility complexes." Piguet V., Wan L., Borel C., Mangasarian A., Demaurex N., Thomas G., Trono D. Nat. Cell Biol. 2:163-167(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH HOST PACS1, SUBCELLULAR LOCATION. Strain: Isolate HXB2-R7.
[7]	"HIV-1 Nef impairs MHC class II antigen presentation and surface expression." Stumptner-Cuvelette P., Morchoisne S., Dugast M., Le Gall S., Raposo G., Schwartz O., Benaroch P. Proc. Natl. Acad. Sci. U.S.A. 98:12144-12149(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"HIV-1 Nef downregulates MHC-I by a PACS-1- and PI3K-regulated ARF6 endocytic pathway." Blagoveshchenskaya A.D., Thomas L., Feliciangeli S.F., Hung C.-H., Thomas G. Cell 111:853-866(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF MET-20; 63-GLU--GLU-65; PRO-72 AND PRO-75. Strain: Isolate HXB2D.
[9]	"HIV-1 Nef disrupts MHC-I trafficking by recruiting AP-1 to the MHC-I cytoplasmic tail." Roeth J.F., Williams M., Kasper M.R., Filzen T.M., Collins K.L. J. Cell Biol. 167:903-913(2004) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A AP1-NEF-MHC-I COMPLEX.
[10]	"Functional characterization of the human immunodeficiency virus type 1 Nef acidic domain." Baugh L.L., Garcia J.V., Foster J.L. J. Virol. 82:9657-9667(2008) [PubMed] [Europe PMC] [Abstract] Cited for: ACIDIC REGION, INTERACTION WITH HOST PACS1, MUTAGENESIS OF 62-GLU--GLU-65.
[11]	"HIV-1 Nef binds PACS-2 to assemble a multikinase cascade that triggers major histocompatibility complex class I (MHC-I) down-regulation: analysis using short interfering RNA and knock-out mice." Atkins K.M., Thomas L., Youker R.T., Harriff M.J., Pissani F., You H., Thomas G. J. Biol. Chem. 283:11772-11784(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HOST PACS2, INTERACTION WITH HOST PACS1, MUTAGENESIS OF 62-GLU--GLU-65.
[12]	"The tyrosine binding pocket in the adaptor protein 1 (AP-1) mu1 subunit is necessary for Nef to recruit AP-1 to the major histocompatibility complex class I cytoplasmic tail." Wonderlich E.R., Williams M., Collins K.L. J. Biol. Chem. 283:3011-3022(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN A AP1(MU)-NEF-MHC-I COMPLEX.
[13]	"Human immunodeficiency virus type 1 Nef incorporation into virions does not increase infectivity." Laguette N., Benichou S., Basmaciogullari S. J. Virol. 83:1093-1104(2009) [PubMed] [Europe PMC] [Abstract] Cited for: CLEAVAGE BY VIRAL PROTEASE.
[14]	"HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4(+) T cells." Lenassi M., Cagney G., Liao M., Vaupotic T., Bartholomeeusen K., Cheng Y., Krogan N.J., Plemenitas A., Peterlin B.M. Traffic 11:110-122(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[15]	"An MHC-I cytoplasmic domain/HIV-1 Nef fusion protein binds directly to the mu subunit of the AP-1 endosomal coat complex." Singh R.K., Lau D., Noviello C.M., Ghosh P., Guatelli J.C. PLoS ONE 4:E8364-E8364(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN A AP1(MU)-NEF-MHC-I COMPLEX.
+	Additional computationally mapped references.

Web resources

BioAfrica HIV proteomics resource

Nef entry

Cross-references

Sequence databases
EMBL GenBank DDBJ	X03187 Genomic RNA. Translation: CAA26946.1. Sequence problems. K03455 Genomic RNA. Translation: AAB50263.1. Sequence problems. AF033819 Genomic RNA. Translation: AAC82597.1. Sequence problems.
RefSeq	NP_057857.2. NC_001802.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	P04601. 8 interactions.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	156110.
Enzyme and pathway databases
Pathway_Interaction_DB	hivnefpathway. HIV-1 Nef: Negative effector of Fas and TNF-alpha.
Reactome	REACT_116125. Disease.
Family and domain databases
Gene3D	3.30.62.10. 1 hit.
InterPro	IPR001558. HIV_Nef. [Graphical view]
Pfam	PF00469. F-protein. 1 hit. [Graphical view]
SUPFAM	SSF55671. HIV_Nef. 1 hit.
ProtoNet	Search...

Entry information

Entry name

NEF_HV1H2

Accession

Primary (citable) accession number: P04601
Secondary accession number(s): O09780, Q85587

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	February 9, 2010
Last modified:	April 3, 2013
This is version 108 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program