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Protein

Protein Nef

Gene

nef

Organism
Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) (HIV-1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.By similarity
In infected CD4+ T-lymphocytes, down-regulates the surface MHC-I, mature MHC-II, CD4, CD28, CCR5 and CXCR4 molecules (By similarity). 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 (By similarity). 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). Down-regulates host SERINC3 and SERINC5 thereby excluding these proteins from the viral particles. Virion infectivity is drastically higher when SERINC3 or SERINC5 are excluded from the viral envelope, because these host antiviral proteins impare the membrane fusion event necessary for subsequent virion penetration.By similarity
Bypasses host T-cell signaling by inducing a transcriptional program nearly identical to that of anti-CD3 cell activation (By similarity). Interaction with TCR-zeta chain up-regulates the Fas ligand (FasL) (PubMed:10224289). Increasing surface FasL molecules and decreasing surface MHC-I molecules on infected CD4+ cells send attacking cytotoxic CD8+ T-lymphocytes into apoptosis (PubMed:10224289).By similarity1 Publication
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/ASK1 (By similarity). Decreases the half-life of TP53, protecting the infected cell against p53-mediated apoptosis (By similarity). 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 (PubMed:11689886).By similarity1 Publication
Extracellular Nef protein targets CD4+ T-lymphocytes for apoptosis by interacting with CXCR4 surface receptors (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei20 – 201Might play a role in AP-1 recruitment to the Nef-MHC-I complexBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Apoptosis, Host-virus interaction, Inhibition of host adaptive immune response by virus, Inhibition of host autophagy by virus, Inhibition of host MHC class I molecule presentation by virus, Inhibition of host MHC class II molecule presentation by virus, Viral immunoevasion, Virulence

Names & Taxonomyi

Protein namesi
Recommended name:
Protein Nef
Alternative name(s):
3'ORF
Negative factor
Short name:
F-protein
Cleaved into the following chain:
Gene namesi
Name:nef
OrganismiHuman immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) (HIV-1)
Taxonomic identifieri11685 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007688 Componenti: Genome

Subcellular locationi

  • Host cell membrane By similarity; Lipid-anchor By similarity; Cytoplasmic side By similarity
  • Virion By similarity
  • Secreted By similarity
  • Host Golgi apparatus membrane By similarity

  • Note: TGN localization requires PACS1. Associates with the inner plasma membrane through its N-terminal domain. Nef stimulates its own export via the release of exosomes. Incorporated in virions at a rate of about 10 molecules per virion, where it is cleaved.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host cell membrane, Host Golgi apparatus, Host membrane, Membrane, Secreted, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi75 – 751R → T: Complete loss of viral replication. Incapacity to trigger cellular activation, probably due to reduced interaction with the TCR environment. 1 Publication
Mutagenesisi107 – 1071S → A: No effect. 1 Publication
Mutagenesisi168 – 1692LL → AA: Partial loss of binding to NBP1. 1 Publication
Mutagenesisi178 – 1792ED → AA: Partial loss of binding to NBP1. 1 Publication

Keywords - Diseasei

AIDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved; by hostBy similarity
Chaini2 – 210209Protein NefPRO_0000038333Add
BLAST
Chaini62 – 210149C-terminal core proteinBy similarityPRO_0000038334Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity
Modified residuei6 – 61Phosphoserine; by host1 Publication

Post-translational modificationi

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).By similarity
Myristoylated.By similarity
Phosphorylated on serine residues, probably by host PKCdelta and theta.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei61 – 622Cleavage; by viral proteaseBy similarity

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Expressioni

Keywords - Developmental stagei

Early protein

Interactioni

Subunit structurei

Monomer; cytosolic form (PubMed:16475823). Homodimer; membrane bound form (PubMed:16475823). Interacts with Nef associated p21-activated kinase (PAK2); this interaction activates PAK2 (PubMed:11070003). Associates with the Nef-MHC-I-AP1 complex; this complex is required for MHC-I internalization (By similarity). Interacts (via C-terminus) with host PI3-kinase (via C-terminus) (PubMed:11689886, PubMed:12009866). Interacts with host PACS1; this interaction seems to be weak (By similarity). Interacts with host PACS2 (By similarity). Interacts with host LCK and MAPK3; these interactions inhibit the kinase activity of the latters (By similarity). Interacts with host ATP6V1H; this interaction may play a role in CD4 endocytosis (By similarity). Associates with the CD4-Nef-AP2 complex; this complex is required for CD4 internalization (By similarity). Interacts with host AP2 subunit alpha and AP2 subunit sigma2 (By similarity). Interacts with TCR-zeta chain; this interaction up-regulates the Fas ligand (FasL) surface expression (PubMed:10224289). Interacts with host HCK, LYN, and SRC; these interactions activate the Src family kinases (PubMed:16849330, PubMed:25122770). Interacts with MAP3K5; this interaction inhibits the Fas and TNFR-mediated death signals (By similarity). Interacts with beta-COP and PTE1. Interacts with human RACK1; this increases Nef phosphorylation by PKC (By similarity). Interacts with TP53; this interaction decreases the half-life of TP53, protecting the infected cell against p53-mediated apoptosis (By similarity).By similarity7 Publications

Protein-protein interaction databases

DIPiDIP-29212N.
IntActiP03407. 2 interactions.
MINTiMINT-1206762.

Structurei

Secondary structure

1
210
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi60 – 7011Combined sources
Helixi85 – 9511Combined sources
Helixi108 – 12215Combined sources
Beta strandi134 – 1363Combined sources
Beta strandi140 – 1423Combined sources
Beta strandi147 – 1515Combined sources
Helixi166 – 1694Combined sources
Helixi171 – 1733Combined sources
Helixi180 – 1823Combined sources
Beta strandi185 – 1895Combined sources
Helixi191 – 1944Combined sources
Helixi198 – 2025Combined sources
Helixi204 – 2063Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RBBX-ray2.35A/C45-210[»]
3REAX-ray2.00A/C45-210[»]
3REBX-ray3.45A/C45-210[»]
4ORZX-ray2.00B45-209[»]
4U1KX-ray2.09C/F75-83[»]
4U1LX-ray2.06C/F75-83[»]
4U1MX-ray1.18C75-83[»]
4U1NX-ray1.77C75-83[»]
4U5WX-ray1.86A/C62-209[»]
ProteinModelPortaliP03407.
SMRiP03407. Positions 2-209.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03407.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni66 – 694Acidic; interacts with host PACS1 and PACS2; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalizationBy similarity
Regioni73 – 8210SH3-binding; interaction with Src family tyrosine kinasesBy similarity
Regioni112 – 12817Mediates dimerization, Nef-PTE1 interaction, Nef-induced CD4 and MHC-I down-regulation and enhancement of infectivityBy similarityAdd
BLAST
Regioni152 – 18433Binding to ATP6V1H1 PublicationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi76 – 794PxxP; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalizationBy similarity
Motifi168 – 1692Dileucine internalization motif; necessary for CD4 internalization1 Publication
Motifi178 – 1792Diacidic; necessary for CD4 internalizationBy similarity

Domaini

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 dileucine internalization motif and a diacidic motif seem to be required for binding to AP-2.By similarity
The acidic region binds to the sorting protein PACS-2, which targets Nef to the paranuclear region, enabling the PxxP motif to direct assembly of an SFK/ZAP-70/PI3K complex that accelerates endocytosis of cell-surface MHC-I.By similarity

Sequence similaritiesi

Keywords - Domaini

SH3-binding

Family and domain databases

Gene3Di3.30.62.10. 1 hit.
4.10.890.10. 1 hit.
InterProiIPR027480. HIV-1_Nef_anchor.
IPR027481. HIV-1_Nef_core.
IPR001558. HIV_Nef.
[Graphical view]
PfamiPF00469. F-protein. 1 hit.
[Graphical view]
SUPFAMiSSF55671. SSF55671. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P03407-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGGKWSKRSM GGWSAIRERM RRAEPRAEPA ADGVGAVSRD LEKHGAITSS
60 70 80 90 100
NTAATNADCA WLEAQEEEEV GFPVRPQVPL RPMTYKAALD ISHFLKEKGG
110 120 130 140 150
LEGLIWSQRR QEILDLWIYH TQGYFPDWQN YTPGPGIRYP LTFGWCFKLV
160 170 180 190 200
PVEPEKVEEA NEGENNSLLH PMSLHGMEDA EKEVLVWRFD SKLAFHHMAR
210
ELHPEYYKDC
Length:210
Mass (Da):24,042
Last modified:January 23, 2007 - v3
Checksum:iED255233F8A17DAB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02007 Genomic RNA. Translation: AAB59883.1.
PIRiA04009. ASLJO2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02007 Genomic RNA. Translation: AAB59883.1.
PIRiA04009. ASLJO2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RBBX-ray2.35A/C45-210[»]
3REAX-ray2.00A/C45-210[»]
3REBX-ray3.45A/C45-210[»]
4ORZX-ray2.00B45-209[»]
4U1KX-ray2.09C/F75-83[»]
4U1LX-ray2.06C/F75-83[»]
4U1MX-ray1.18C75-83[»]
4U1NX-ray1.77C75-83[»]
4U5WX-ray1.86A/C62-209[»]
ProteinModelPortaliP03407.
SMRiP03407. Positions 2-209.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29212N.
IntActiP03407. 2 interactions.
MINTiMINT-1206762.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP03407.

Family and domain databases

Gene3Di3.30.62.10. 1 hit.
4.10.890.10. 1 hit.
InterProiIPR027480. HIV-1_Nef_anchor.
IPR027481. HIV-1_Nef_core.
IPR001558. HIV_Nef.
[Graphical view]
PfamiPF00469. F-protein. 1 hit.
[Graphical view]
SUPFAMiSSF55671. SSF55671. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Induction of phosphorylation of human immunodeficiency virus type 1 Nef and enhancement of CD4 down-regulation by phorbol myristate acetate."
    Luo T., Downing J.R., Garcia J.V.
    J. Virol. 71:2535-2539(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION, MUTAGENESIS OF SER-107.
  3. "SH3-mediated Hck tyrosine kinase activation and fibroblast transformation by the Nef protein of HIV-1."
    Briggs S.D., Sharkey M., Stevenson M., Smithgall T.E.
    J. Biol. Chem. 272:17899-17902(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "Interactions between HIV1 Nef and vacuolar ATPase facilitate the internalization of CD4."
    Lu X., Yu H., Liu S.-H., Brodsky F.M., Peterlin B.M.
    Immunity 8:647-656(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN ATP6V1H.
  5. "Induction of Fas ligand expression by HIV involves the interaction of Nef with the T cell receptor zeta chain."
    Xu X.-N., Laffert B., Screaton G.R., Kraft M., Wolf D., Kolanus W., Mongkolsapay J., McMichael A.J., Baur A.S.
    J. Exp. Med. 189:1489-1496(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH HOST TCR-ZETA CHAIN/TCR-ZETA.
  6. "HIV-1 Nef plays an essential role in two independent processes in CD4 down-regulation: dissociation of the CD4-p56(lck) complex and targeting of CD4 to lysosomes."
    Kim Y.-H., Chang S.H., Kwon J.H., Rhee S.S.
    Virology 257:208-219(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. Cited for: FUNCTION, INTERACTION WITH PAK2.
  8. "Nef triggers a transcriptional program in T cells imitating single-signal T cell activation and inducing HIV virulence mediators."
    Simmons A., Aluvihare V., McMichael A.
    Immunity 14:763-777(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "HIV-1 Nef associated PAK and PI3-kinases stimulate Akt-independent Bad-phosphorylation to induce anti-apoptotic signals."
    Wolf D., Witte V., Laffert B., Blume K., Stromer E., Trapp S., d'Aloja P., Schuermann A., Baur A.S.
    Nat. Med. 7:1217-1224(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN A NEF/PI3-KINASE/PAK2 COMPLEX.
  10. "A natural variability in the proline-rich motif of Nef modulates HIV-1 replication in primary T cells."
    Fackler O.T., Wolf D., Weber H.O., Laffert B., D'Aloja P., Schuler-Thurner B., Geffin R., Saksela K., Geyer M., Peterlin B.M., Schuler G., Baur A.S.
    Curr. Biol. 11:1294-1299(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-75.
  11. "Interaction between Nef and phosphatidylinositol-3-kinase leads to activation of p21-activated kinase and increased production of HIV."
    Linnemann T., Zheng Y.-H., Mandic R., Peterlin B.M.
    Virology 294:246-255(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN PI3-KINASE.
  12. "Subunit H of the V-ATPase involved in endocytosis shows homology to beta-adaptins."
    Geyer M., Fackler O.T., Peterlin B.M.
    Mol. Biol. Cell 13:2045-2056(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN ATP6V1H, MUTAGENESIS OF 168-LEU-LEU-169 AND 178-GLU-ASP-179.
  13. "Subunit H of the V-ATPase binds to the medium chain of adaptor protein complex 2 and connects Nef to the endocytic machinery."
    Geyer M., Yu H., Mandic R., Linnemann T., Zheng Y.-H., Fackler O.T., Peterlin B.M.
    J. Biol. Chem. 277:28521-28529(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN ATP6V1H.
  14. "HIV-1 Nef selectively activates Src family kinases Hck, Lyn, and c-Src through direct SH3 domain interaction."
    Trible R.P., Emert-Sedlak L., Smithgall T.E.
    J. Biol. Chem. 281:27029-27038(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SH3-BINDING MOTIF, FUNCTION, INTERACTION WITH HOST HCK, INTERACTION WITH HOST LYN, INTERACTION WITH HOST SRC.
  15. "Biochemical indication for myristoylation-dependent conformational changes in HIV-1 Nef."
    Breuer S., Gerlach H., Kolaric B., Urbanke C., Opitz N., Geyer M.
    Biochemistry 45:2339-2349(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  16. "Novel (n)PKC kinases phosphorylate Nef for increased HIV transcription, replication and perinuclear targeting."
    Wolf D., Giese S.I., Witte V., Krautkraemer E., Trapp S., Sass G., Haller C., Blume K., Fackler O.T., Baur A.S.
    Virology 370:45-54(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-6.
  17. "Conformation of the dileucine-based sorting motif in HIV-1 Nef revealed by intermolecular domain assembly."
    Horenkamp F.A., Breuer S., Schulte A., Lulf S., Weyand M., Saksela K., Geyer M.
    Traffic 12:867-877(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 45-210, DILEUCINE MOTIF.
  18. "Interaction with the Src homology (SH3-SH2) region of the Src-family kinase Hck structures the HIV-1 Nef dimer for kinase activation and effector recruitment."
    Alvarado J.J., Tarafdar S., Yeh J.I., Smithgall T.E.
    J. Biol. Chem. 289:28539-28553(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.86 ANGSTROMS) OF 62-209, INTERACTION WITH HOST HCK.

Entry informationi

Entry nameiNEF_HV1A2
AccessioniPrimary (citable) accession number: P03407
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 127 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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).

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.