Database: UniProt
Entry: Q90VU7
LinkDB: Q90VU7
Original site: Q90VU7 
ID   Q90VU7_9HIV1            Unreviewed;       206 AA.
AC   Q90VU7;
DT   01-DEC-2001, integrated into UniProtKB/TrEMBL.
DT   01-DEC-2001, sequence version 1.
DT   12-AUG-2020, entry version 133.
DE   RecName: Full=Protein Nef {ECO:0000256|HAMAP-Rule:MF_04078};
DE   AltName: Full=3'ORF {ECO:0000256|HAMAP-Rule:MF_04078};
DE   AltName: Full=Negative factor {ECO:0000256|HAMAP-Rule:MF_04078};
DE            Short=F-protein {ECO:0000256|HAMAP-Rule:MF_04078};
DE   Contains:
DE     RecName: Full=C-terminal core protein {ECO:0000256|HAMAP-Rule:MF_04078};
GN   Name=nef {ECO:0000256|HAMAP-Rule:MF_04078,
GN   ECO:0000313|EMBL:AAB60579.1};
OS   Human immunodeficiency virus 1.
OC   Viruses; Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
OX   NCBI_TaxID=11676 {ECO:0000313|EMBL:AAB60579.1, ECO:0000313|Proteomes:UP000160754};
OH   NCBI_TaxID=9606; Homo sapiens (Human).
RN   [1] {ECO:0000313|EMBL:AAB60579.1, ECO:0000313|Proteomes:UP000160754}
RC   STRAIN=NL4-3 {ECO:0000313|EMBL:AAB60579.1};
RX   PubMed=3016298;
RA   Adachi A., Gendelman H.E., Koenig S., Folks T., Willey R., Rabson A.,
RA   Martin M.A.;
RT   "Production of acquired immunodeficiency syndrome-associated retrovirus in
RT   human and nonhuman cells transfected with an infectious molecular clone.";
RL   J. Virol. 59:284-291(1986).
RN   [2] {ECO:0000313|EMBL:AAB60579.1, ECO:0000313|Proteomes:UP000160754}
RC   STRAIN=NL4-3 {ECO:0000313|EMBL:AAB60579.1};
RX   PubMed=7483282; DOI=10.1006/viro.1995.1548;
RA   Salminen M.O., Koch C., Sanders-Buell E., Ehrenberg P.K., Michael N.L.,
RA   Carr J.K., Burke D.S., McCutchan F.E.;
RT   "Recovery of virtually full-length HIV-1 provirus of diverse subtypes from
RT   primary virus cultures using the polymerase chain reaction.";
RL   Virology 213:80-86(1995).
RN   [3] {ECO:0000313|EMBL:AAB60579.1}
RC   STRAIN=NL4-3 {ECO:0000313|EMBL:AAB60579.1};
RA   Salminen M.S.;
RL   Submitted (MAY-1995) to the EMBL/GenBank/DDBJ databases.
RN   [4] {ECO:0000313|EMBL:CAH64567.1}
RX   PubMed=16032733; DOI=10.1002/jmv.20408;
RA   Parreira R., Padua E., Piedade J., Venenno T., Paixao M.T., Esteves A.;
RT   "Genetic analysis of human immunodeficiency virus type 1 nef in Portugal:
RT   subtyping, identification of mosaic genes, and amino acid sequence
RT   variability.";
RL   J. Med. Virol. 77:8-16(2005).
RN   [5] {ECO:0000313|EMBL:ABY49078.1}
RC   STRAIN=184003/B8 {ECO:0000313|EMBL:ABY49078.1};
RX   PubMed=18184702; DOI=10.1128/JVI.02260-07;
RA   Turk G., Gherardi M.M., Laufer N., Saracco M., Luzzi R., Cox J.H., Cahn P.,
RA   Salomon H.;
RT   "Magnitude, breadth, and functional profile of T-cell responses during
RT   human immunodeficiency virus primary infection with B and BF viral
RT   variants.";
RL   J. Virol. 82:2853-2866(2008).
RN   [6] {ECO:0000313|EMBL:ACM50127.1}
RC   STRAIN=F781 {ECO:0000313|EMBL:ACM50127.1};
RX   PubMed=19036810; DOI=10.1128/JVI.01061-08;
RA   Wang Y.E., Li B., Carlson J.M., Streeck H., Gladden A.D., Goodman R.,
RA   Schneidewind A., Power K.A., Toth I., Frahm N., Alter G., Brander C.,
RA   Carrington M., Walker B.D., Altfeld M., Heckerman D., Allen T.M.;
RT   "Protective HLA class I alleles that restrict acute-phase CD8+ T-cell
RT   responses are associated with viral escape mutations located in highly
RT   conserved regions of human immunodeficiency virus type 1.";
RL   J. Virol. 83:1845-1855(2009).
RN   [7] {ECO:0000313|EMBL:ADB03681.1}
RC   STRAIN=BEC73 {ECO:0000313|EMBL:ADB03681.1};
RA   Miura T., Brumme C.J., Brockman M.A., Brumme Z.L., Pereyra F., Block B.L.,
RA   Trocha A., John M., Mallal S., Harrigan P.R., Walker B.D.;
RT   "HLA-associated viral mutations are common in Human immunodeficiency virus
RT   type 1 elite controllers.";
RL   J. Virol. 84:1212-1212(2010).
RN   [8] {ECO:0000313|EMBL:ADJ17496.1}
RC   STRAIN=5569.6 {ECO:0000313|EMBL:ADJ17498.1}, 5569.7
RC   {ECO:0000313|EMBL:ADJ17499.1}, 5569.81 {ECO:0000313|EMBL:ADJ17500.1},
RC   5569.82 {ECO:0000313|EMBL:ADJ17501.1}, 5569.83
RC   {ECO:0000313|EMBL:ADJ17502.1}, and
RC   {ECO:0000313|EMBL:ADJ17496.1};
RX   PubMed=20463068; DOI=10.1128/JVI.00619-10;
RA   Specht A., Telenti A., Martinez R., Fellay J., Bailes E., Evans D.T.,
RA   Carrington M., Hahn B.H., Goldstein D.B., Kirchhoff F.;
RT   "Counteraction of HLA-C-mediated immune control of HIV-1 by Nef.";
RL   J. Virol. 84:7300-7311(2010).
RN   [9] {ECO:0000213|PDB:4EMZ, ECO:0000213|PDB:4EN2}
RX   PubMed=22705789; DOI=10.1038/nsmb.2328;
RA   Jia X., Singh R., Homann S., Yang H., Guatelli J., Xiong Y.;
RT   "Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef.";
RL   Nat. Struct. Mol. Biol. 19:701-706(2012).
RN   [10] {ECO:0000313|EMBL:AFM44079.1, ECO:0000313|Proteomes:UP000114822}
RC   STRAIN=HIV/US/BID-V4141 {ECO:0000313|EMBL:AFM44079.1};
RX   PubMed=22412369; DOI=10.1371/journal.ppat.1002529;
RA   Henn M.R., Boutwell C.L., Charlebois P., Lennon N.J., Power K.A.,
RA   Macalalad A.R., Berlin A.M., Malboeuf C.M., Ryan E.M., Gnerre S.,
RA   Zody M.C., Erlich R.L., Green L.M., Berical A., Wang Y., Casali M.,
RA   Streeck H., Bloom A.K., Dudek T., Tully D., Newman R., Axten K.L.,
RA   Gladden A.D., Battis L., Kemper M., Zeng Q., Shea T.P., Gujja S.,
RA   Zedlack C., Gasser O., Brander C., Hess C., Gunthard H.F., Brumme Z.L.,
RA   Brumme C.J., Bazner S., Rychert J., Tinsley J.P., Mayer K.H., Rosenberg E.,
RA   Pereyra F., Levin J.Z., Young S.K., Jessen H., Altfeld M., Birren B.W.,
RA   Walker B.D., Allen T.M.;
RT   "Whole genome deep sequencing of HIV-1 reveals the impact of early minor
RT   variants upon immune recognition during acute infection.";
RL   PLoS Pathog. 8:E1002529-E1002529(2012).
RN   [11] {ECO:0000313|EMBL:AGV32938.1}
RC   STRAIN=16CB1_20F5 {ECO:0000313|EMBL:AGV32938.1}, 16CB1_20F7
RC   {ECO:0000313|EMBL:AGV32939.1}, and 22CB6_23G3
RC   {ECO:0000313|EMBL:AGV33378.1};
RA   Ho Y.-C., Shan L., Hosmane N.N., Wang J., Laskey S.B., Rosenbloom D.I.,
RA   Lai J., Blankson J.N., Siliciano R.F.;
RT   "Replication-competent non-induced proviruses in the latent reservoir
RT   increase barrier to HIV-1 cure.";
RL   Submitted (AUG-2013) to the EMBL/GenBank/DDBJ databases.
RN   [12] {ECO:0000313|EMBL:AIW80604.1}
RA   Whitcomb J.;
RT   "Reference sequence used by Monogram Biosciences for genotyping assays of
RT   HIV.";
RL   Submitted (AUG-2014) to the EMBL/GenBank/DDBJ databases.
RN   [13] {ECO:0000313|EMBL:AKR15819.1}
RC   STRAIN=FP_24 {ECO:0000313|EMBL:AKR15834.1}, FP_25
RC   {ECO:0000313|EMBL:AKR15835.1}, FP_26 {ECO:0000313|EMBL:AKR15836.1},
RC   FP_27 {ECO:0000313|EMBL:AKR15837.1}, FP_28
RC   {ECO:0000313|EMBL:AKR15838.1}, FP_29 {ECO:0000313|EMBL:AKR15839.1},
RC   FP_30 {ECO:0000313|EMBL:AKR15840.1}, FP_31
RC   {ECO:0000313|EMBL:AKR15841.1}, FP_32 {ECO:0000313|EMBL:AKR15842.1},
RC   LTNP_4 {ECO:0000313|EMBL:AKR15819.1}, LTNP_7
RC   {ECO:0000313|EMBL:AKR15822.1}, LTNP_8 {ECO:0000313|EMBL:AKR15823.1},
RC   LTNP_9 {ECO:0000313|EMBL:AKR15824.1}, SP_11
RC   {ECO:0000313|EMBL:AKR15825.1}, SP_12 {ECO:0000313|EMBL:AKR15826.1},
RC   SP_13 {ECO:0000313|EMBL:AKR15827.1}, SP_14
RC   {ECO:0000313|EMBL:AKR15828.1}, SP_15 {ECO:0000313|EMBL:AKR15829.1},
RC   SP_19 {ECO:0000313|EMBL:AKR15830.1}, SP_20
RC   {ECO:0000313|EMBL:AKR15831.1}, SP_22 {ECO:0000313|EMBL:AKR15832.1},
RC   SP_23 {ECO:0000313|EMBL:AKR15833.1}, SP_5
RC   {ECO:0000313|EMBL:AKR15820.1}, and SP_6 {ECO:0000313|EMBL:AKR15821.1};
RA   Kondapi A.K., Rao S.K., Bommakanti A.;
RT   "Analysis of human immunodeficiency virus type-1 nef sequences in
RT   paediatric seropositive population.";
RL   Submitted (FEB-2015) to the EMBL/GenBank/DDBJ databases.
RN   [14] {ECO:0000313|EMBL:AKZ17633.1}
RA   Singh J., Ronsard L., Ramachandran V.G., Banerjea A.C.;
RT   "Genetic and functional characterization of HIV-1 nef gene.";
RL   Submitted (MAY-2015) to the EMBL/GenBank/DDBJ databases.
RN   [15] {ECO:0000213|PDB:6CM9, ECO:0000213|PDB:6D83, ECO:0000213|PDB:6D84}
RX   PubMed=30053425; DOI=10.1016/j.cell.2018.07.004;
RA   Morris K.L., Buffalo C.Z., Sturzel C.M., Heusinger E., Kirchhoff F.,
RA   Ren X., Hurley J.H.;
RT   "HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin
RT   Downregulation.";
RL   Cell 174:659-671.e14(2018).
RN   [16] {ECO:0000313|EMBL:QCS35511.1}
RC   STRAIN=Strain0526 {ECO:0000313|EMBL:QCS35511.1};
RX   PubMed=30939815;
RA   Banin A.N., Tuen M., Bimela J.S., Tongo M., Zappile P.,
RA   Khodadadi-Jamayran A., Nanfack A.J., Meli J., Wang X., Mbanya D.,
RA   Ngogang J., Heguy A., Nyambi P.N., Fokunang C., Duerr R.;
RT   "Development of a Versatile, Near Full Genome Amplification and Sequencing
RT   Approach for a Broad Variety of HIV-1 Group M Variants.";
RL   Viruses 11:0-E317(2019).
CC   -!- FUNCTION: Bypasses host T-cell signaling by inducing a transcriptional
CC       program nearly identical to that of anti-CD3 cell activation.
CC       Interaction with TCR-zeta chain up-regulates the Fas ligand (FasL).
CC       Increasing surface FasL molecules and decreasing surface MHC-I
CC       molecules on infected CD4(+) cells send attacking cytotoxic CD8+ T-
CC       lymphocytes into apoptosis. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- FUNCTION: Extracellular Nef protein targets CD4(+) T-lymphocytes for
CC       apoptosis by interacting with CXCR4 surface receptors.
CC       {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- FUNCTION: Factor of infectivity and pathogenicity, required for optimal
CC       virus replication. Alters numerous pathways of T-lymphocytes function
CC       and down-regulates immunity surface molecules in order to evade host
CC       defense and increase viral infectivity. Alters the functionality of
CC       other immunity cells, like dendritic cells, monocytes/macrophages and
CC       NK cells. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- FUNCTION: In infected CD4(+) T-lymphocytes, down-regulates the surface
CC       MHC-I, mature MHC-II, CD4, CD28, CCR5 and CXCR4 molecules. Mediates
CC       internalization and degradation of host CD4 through the interaction of
CC       with the cytoplasmic tail of CD4, the recruitment of AP-2 (clathrin
CC       adapter protein complex 2), internalization through clathrin coated
CC       pits, and subsequent transport to endosomes and lysosomes for
CC       degradation. Diverts host MHC-I molecules to the trans-Golgi network-
CC       associated endosomal compartments by an endocytic pathway to finally
CC       target them for degradation. MHC-I down-regulation may involve AP-1
CC       (clathrin adapter protein complex 1) or possibly Src family kinase-
CC       ZAP70/Syk-PI3K cascade recruited by PACS2. In consequence infected
CC       cells are masked for immune recognition by cytotoxic T-lymphocytes.
CC       Decreasing the number of immune receptors also prevents reinfection by
CC       more HIV particles (superinfection). Down-regulates host SERINC3 and
CC       SERINC5 thereby excluding these proteins from the viral particles.
CC       Virion infectivity is drastically higher when SERINC3 or SERINC5 are
CC       excluded from the viral envelope, because these host antiviral proteins
CC       impare the membrane fusion event necessary for subsequent virion
CC       penetration. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- FUNCTION: Plays a role in optimizing the host cell environment for
CC       viral replication without causing cell death by apoptosis. Protects the
CC       infected cells from apoptosis in order to keep them alive until the
CC       next virus generation is ready to strike. Inhibits the Fas and TNFR-
CC       mediated death signals by blocking MAP3K5/ASK1. Decreases the half-life
CC       of TP53, protecting the infected cell against p53-mediated apoptosis.
CC       Inhibits the apoptotic signals regulated by the Bcl-2 family proteins
CC       through the formation of a Nef/PI3-kinase/PAK2 complex that leads to
CC       activation of PAK2 and induces phosphorylation of host BAD.
CC       {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- SUBUNIT: Monomer; cytosolic form. Homodimer; membrane bound form.
CC       Interacts with Nef associated p21-activated kinase (PAK2); this
CC       interaction activates PAK2. Associates with the Nef-MHC-I-AP1 complex;
CC       this complex is required for MHC-I internalization. Interacts (via C-
CC       terminus) with host PI3-kinase. Interacts with host PACS1; this
CC       interaction seems to be weak. Interacts with host PACS2. Interacts with
CC       host LCK and MAPK3; these interactions inhibit the kinase activity of
CC       the latters. Interacts with host ATP6V1H; this interaction may play a
CC       role in CD4 endocytosis. Associates with the CD4-Nef-AP2 complex; this
CC       complex is required for CD4 internalization. Interacts with host AP2
CC       subunit alpha and AP2 subunit sigma2. Interacts with TCR-zeta chain;
CC       this interaction up-regulates the Fas ligand (FasL) surface expression.
CC       Interacts with host HCK, LYN, and SRC; these interactions activate the
CC       Src family kinases. Interacts with MAP3K5; this interaction inhibits
CC       the Fas and TNFR-mediated death signals. Interacts with beta-COP and
CC       PTE1. Interacts with human RACK1; this increases Nef phosphorylation by
CC       PKC. Interacts with TP53; this interaction decreases the half-life of
CC       TP53, protecting the infected cell against p53-mediated apoptosis.
CC       {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- SUBCELLULAR LOCATION: Host cell membrane {ECO:0000256|HAMAP-
CC       Rule:MF_04078}; Lipid-anchor {ECO:0000256|HAMAP-Rule:MF_04078};
CC       Cytoplasmic side {ECO:0000256|HAMAP-Rule:MF_04078}. Virion
CC       {ECO:0000256|HAMAP-Rule:MF_04078}. Secreted {ECO:0000256|HAMAP-
CC       Rule:MF_04078}. Host Golgi apparatus membrane {ECO:0000256|HAMAP-
CC       Rule:MF_04078}. Note=TGN localization requires PACS1. Associates with
CC       the inner plasma membrane through its N-terminal domain. Nef stimulates
CC       its own export via the release of exosomes. Incorporated in virions at
CC       a rate of about 10 molecules per virion, where it is cleaved.
CC       {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- INDUCTION: Expressed early in the viral replication cycle.
CC       {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- DOMAIN: The N-terminal domain is composed of the N-myristoyl glycine
CC       and of a cluster of positively charged amino acids. It is required for
CC       inner plasma membrane targeting of Nef and virion incorporation, and
CC       thereby for infectivity. This domain is also involved in binding to
CC       TP53. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- DOMAIN: The SH3-binding domain constituted of PxxP motifs mediates
CC       binding to several Src family proteins thereby regulating their
CC       tyrosine kinase activity. The same motifs also mediates the association
CC       with MAPK3, PI3-kinase and TCR-zeta. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- DOMAIN: The acidic region binds to the sorting protein PACS-2, which
CC       targets Nef to the paranuclear region, enabling the PxxP motif to
CC       direct assembly of an SFK/ZAP-70/PI3K complex that accelerates
CC       endocytosis of cell-surface MHC-I. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- DOMAIN: The dileucine internalization motif and a diacidic motif seem
CC       to be required for binding to AP-2. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- PTM: Myristoylated. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- PTM: Phosphorylated on serine residues, probably by host PKCdelta and
CC       theta. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- PTM: The virion-associated Nef proteins are cleaved by the viral
CC       protease to release the soluble C-terminal core protein. Nef is
CC       probably cleaved concomitantly with viral structural proteins on
CC       maturation of virus particles. {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- MISCELLANEOUS: HIV-1 lineages are divided in three main groups, M (for
CC       Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast
CC       majority of strains found worldwide belong to the group M. Group O
CC       seems to be endemic to and largely confined to Cameroon and neighboring
CC       countries in West Central Africa, where these viruses represent a small
CC       minority of HIV-1 strains. The group N is represented by a limited
CC       number of isolates from Cameroonian persons. The group M is further
CC       subdivided in 9 clades or subtypes (A to D, F to H, J and K).
CC       {ECO:0000256|HAMAP-Rule:MF_04078}.
CC   -!- SIMILARITY: Belongs to the lentivirus primate group Nef protein family.
CC       {ECO:0000256|ARBA:ARBA00006933, ECO:0000256|HAMAP-Rule:MF_04078,
CC       ECO:0000256|RuleBase:RU000344}.
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DR   EMBL; U26942; AAB60579.1; -; Genomic_DNA.
DR   EMBL; EU312175; ABY49078.1; -; Genomic_DNA.
DR   EMBL; FJ469736; ACM50127.1; -; Genomic_DNA.
DR   EMBL; GU046594; ADB03681.1; -; Genomic_DNA.
DR   EMBL; HM244488; ADJ17496.1; -; Genomic_RNA.
DR   EMBL; HM244490; ADJ17498.1; -; Genomic_RNA.
DR   EMBL; HM244491; ADJ17499.1; -; Genomic_RNA.
DR   EMBL; HM244492; ADJ17500.1; -; Genomic_RNA.
DR   EMBL; HM244493; ADJ17501.1; -; Genomic_RNA.
DR   EMBL; HM244494; ADJ17502.1; -; Genomic_RNA.
DR   EMBL; JQ403040; AFM44079.1; -; Genomic_RNA.
DR   EMBL; KF526172; AGV32938.1; -; Genomic_DNA.
DR   EMBL; KF526173; AGV32939.1; -; Genomic_DNA.
DR   EMBL; KF526308; AGV33378.1; -; Genomic_DNA.
DR   EMBL; KM390026; AIW80604.1; -; Viral_cRNA.
DR   EMBL; KP851719; AKR15819.1; -; Genomic_DNA.
DR   EMBL; KP851720; AKR15820.1; -; Genomic_DNA.
DR   EMBL; KP851721; AKR15821.1; -; Genomic_DNA.
DR   EMBL; KP851722; AKR15822.1; -; Genomic_DNA.
DR   EMBL; KP851723; AKR15823.1; -; Genomic_DNA.
DR   EMBL; KP851724; AKR15824.1; -; Genomic_DNA.
DR   EMBL; KP851725; AKR15825.1; -; Genomic_DNA.
DR   EMBL; KP851726; AKR15826.1; -; Genomic_DNA.
DR   EMBL; KP851727; AKR15827.1; -; Genomic_DNA.
DR   EMBL; KP851728; AKR15828.1; -; Genomic_DNA.
DR   EMBL; KP851729; AKR15829.1; -; Genomic_DNA.
DR   EMBL; KP851730; AKR15830.1; -; Genomic_DNA.
DR   EMBL; KP851731; AKR15831.1; -; Genomic_DNA.
DR   EMBL; KP851732; AKR15832.1; -; Genomic_DNA.
DR   EMBL; KP851733; AKR15833.1; -; Genomic_DNA.
DR   EMBL; KP851734; AKR15834.1; -; Genomic_DNA.
DR   EMBL; KP851735; AKR15835.1; -; Genomic_DNA.
DR   EMBL; KP851736; AKR15836.1; -; Genomic_DNA.
DR   EMBL; KP851737; AKR15837.1; -; Genomic_DNA.
DR   EMBL; KP851738; AKR15838.1; -; Genomic_DNA.
DR   EMBL; KP851739; AKR15839.1; -; Genomic_DNA.
DR   EMBL; KP851740; AKR15840.1; -; Genomic_DNA.
DR   EMBL; KP851741; AKR15841.1; -; Genomic_DNA.
DR   EMBL; KP851742; AKR15842.1; -; Genomic_DNA.
DR   EMBL; KR818790; AKZ17633.1; -; Genomic_DNA.
DR   EMBL; KR818792; AKZ17634.1; -; Genomic_DNA.
DR   EMBL; AJ850868; CAH64567.1; -; Genomic_DNA.
DR   EMBL; MK086129; QCS35511.1; -; Genomic_RNA.
DR   PIR; JC5400; JC5400.
DR   PIR; JQ1620; JQ1620.
DR   PIR; S03244; S03244.
DR   PIR; S43467; S43467.
DR   PDB; 4EMZ; X-ray; 2.90 A; B/C=1-206.
DR   PDB; 4EN2; X-ray; 2.58 A; B/C=1-206.
DR   PDB; 6CM9; EM; 3.73 A; L/N/T=1-206.
DR   PDB; 6D83; EM; 4.27 A; L/T=1-206.
DR   PDB; 6D84; EM; 6.72 A; L/O/R/T=1-206.
DR   PDB; 6DFF; EM; 3.90 A; L/T=1-206.
DR   PDBsum; 4EMZ; -.
DR   PDBsum; 4EN2; -.
DR   PDBsum; 6CM9; -.
DR   PDBsum; 6D83; -.
DR   PDBsum; 6D84; -.
DR   PDBsum; 6DFF; -.
DR   DIP; DIP-43762N; -.
DR   IntAct; Q90VU7; 13.
DR   Proteomes; UP000114822; Genome.
DR   Proteomes; UP000160754; Genome.
DR   GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR   GO; GO:0044178; C:host cell Golgi membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0020002; C:host cell plasma membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-UniRule.
DR   GO; GO:0019012; C:virion; IEA:UniProtKB-SubCell.
DR   GO; GO:0051117; F:ATPase binding; ISS:UniProtKB.
DR   GO; GO:0042609; F:CD4 receptor binding; ISS:UniProtKB.
DR   GO; GO:0005525; F:GTP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0042288; F:MHC class I protein binding; ISS:UniProtKB.
DR   GO; GO:0019901; F:protein kinase binding; ISS:UniProtKB.
DR   GO; GO:0017124; F:SH3 domain binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0005102; F:signaling receptor binding; ISS:UniProtKB.
DR   GO; GO:0031996; F:thioesterase binding; ISS:UniProtKB.
DR   GO; GO:0045225; P:negative regulation of CD4 biosynthetic process; ISS:UniProtKB.
DR   GO; GO:0009405; P:pathogenesis; ISS:UniProtKB.
DR   GO; GO:0050848; P:regulation of calcium-mediated signaling; ISS:UniProtKB.
DR   GO; GO:0052085; P:suppression by symbiont of host T-cell mediated immune response; ISS:UniProtKB.
DR   GO; GO:0039504; P:suppression by virus of host adaptive immune response; IEA:UniProtKB-UniRule.
DR   GO; GO:0046776; P:suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I; ISS:UniProtKB.
DR   GO; GO:0039505; P:suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II; IEA:UniProtKB-UniRule.
DR   GO; GO:0039521; P:suppression by virus of host autophagy; IEA:UniProtKB-UniRule.
DR   GO; GO:0019058; P:viral life cycle; ISS:UniProtKB.
DR   Gene3D;; -; 1.
DR   Gene3D; 4.10.890.10; -; 1.
DR   HAMAP; MF_04078; NEF_HIV; 1.
DR   InterPro; IPR027480; HIV-1_Nef_anchor_sf.
DR   InterPro; IPR027481; HIV-1_Nef_core_sf.
DR   InterPro; IPR001558; HIV_Nef.
DR   Pfam; PF00469; F-protein; 1.
DR   SUPFAM; SSF55671; SSF55671; 1.
PE   1: Evidence at protein level;
KW   3D-structure {ECO:0000213|PDB:4EMZ, ECO:0000213|PDB:4EN2,
KW   ECO:0000213|PDB:6CM9, ECO:0000213|PDB:6D83};
KW   Apoptosis {ECO:0000256|ARBA:ARBA00022703, ECO:0000256|HAMAP-Rule:MF_04078};
KW   Early protein {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Host cell membrane {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Host Golgi apparatus {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Host membrane {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Host-virus interaction {ECO:0000256|ARBA:ARBA00022581, ECO:0000256|HAMAP-
KW   Rule:MF_04078};
KW   Inhibition of host adaptive immune response by virus {ECO:0000256|HAMAP-
KW   Rule:MF_04078};
KW   Inhibition of host autophagy by virus {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Inhibition of host MHC class I molecule presentation by virus
KW   {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Inhibition of host MHC class II molecule presentation by virus
KW   {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Lipoprotein {ECO:0000256|ARBA:ARBA00023288, ECO:0000256|HAMAP-
KW   Rule:MF_04078, ECO:0000256|RuleBase:RU000344};
KW   Membrane {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Myristate {ECO:0000256|ARBA:ARBA00022707, ECO:0000256|HAMAP-Rule:MF_04078,
KW   ECO:0000256|RuleBase:RU000344};
KW   Phosphoprotein {ECO:0000256|ARBA:ARBA00022553, ECO:0000256|HAMAP-
KW   Rule:MF_04078}; Reference proteome {ECO:0000313|Proteomes:UP000160754};
KW   Secreted {ECO:0000256|HAMAP-Rule:MF_04078};
KW   SH3-binding {ECO:0000256|ARBA:ARBA00023036, ECO:0000256|HAMAP-
KW   Rule:MF_04078};
KW   Viral immunoevasion {ECO:0000256|ARBA:ARBA00023280, ECO:0000256|HAMAP-
KW   Rule:MF_04078, ECO:0000256|RuleBase:RU000344};
KW   Virion {ECO:0000256|HAMAP-Rule:MF_04078};
KW   Virulence {ECO:0000256|ARBA:ARBA00023026, ECO:0000256|HAMAP-Rule:MF_04078,
KW   ECO:0000256|RuleBase:RU000344}.
FT   INIT_MET        1
FT                   /note="Removed; by host"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   CHAIN           2..206
FT                   /note="Protein Nef"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT                   /id="PRO_5025730580"
FT   CHAIN           58..206
FT                   /note="C-terminal core protein"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT                   /id="PRO_5025730579"
FT   REGION          62..65
FT                   /note="Acidic; interacts with host PACS1 and PACS2;
FT                   stabilizes the interaction of NEF/MHC-I with host AP1M1;
FT                   necessary for MHC-I internalization"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   REGION          69..78
FT                   /note="SH3-binding; interaction with Src family tyrosine
FT                   kinases"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   REGION          108..124
FT                   /note="Mediates dimerization, Nef-PTE1 interaction"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   REGION          148..180
FT                   /note="Binding to ATP6V1H"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   MOTIF           72..75
FT                   /note="PxxP; stabilizes the interaction of NEF/MHC-I with
FT                   host AP1M1; necessary for MHC-I internalization"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   MOTIF           164..165
FT                   /note="Dileucine internalization motif; necessary for CD4
FT                   internalization"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   MOTIF           174..175
FT                   /note="Diacidic; necessary for CD4 internalization"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   SITE            20
FT                   /note="Might play a role in AP-1 recruitment to the Nef-
FT                   MHC-I complex"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   SITE            57..58
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   MOD_RES         6
FT                   /note="Phosphoserine; by host"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
FT   LIPID           2
FT                   /note="N-myristoyl glycine; by host"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_04078"
SQ   SEQUENCE   206 AA;  23367 MW;  65AF3B6184DC2FE7 CRC64;
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