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Protein Nef (3'ORF) (Negative factor) (F-protein) [Cleaved into: C-terminal core protein]

 NEF_HV1BR               Reviewed;         206 AA.
P03406;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
25-OCT-2017, entry version 152.
RecName: Full=Protein Nef {ECO:0000255|HAMAP-Rule:MF_04078};
AltName: Full=3'ORF {ECO:0000255|HAMAP-Rule:MF_04078};
AltName: Full=Negative factor {ECO:0000255|HAMAP-Rule:MF_04078};
Short=F-protein {ECO:0000255|HAMAP-Rule:MF_04078};
Contains:
RecName: Full=C-terminal core protein {ECO:0000255|HAMAP-Rule:MF_04078};
Name=nef {ECO:0000255|HAMAP-Rule:MF_04078};
Human immunodeficiency virus type 1 group M subtype B (isolate
BRU/LAI) (HIV-1).
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae;
Lentivirus; Primate lentivirus group.
NCBI_TaxID=11686;
NCBI_TaxID=9606; Homo sapiens (Human).
[1]
NUCLEOTIDE SEQUENCE.
PubMed=2981635; DOI=10.1016/0092-8674(85)90303-4;
Wain-Hobson S., Sonigo P., Danos O., Cole S., Alizon M.;
"Nucleotide sequence of the AIDS virus, LAV.";
Cell 40:9-17(1985).
[2]
NUCLEOTIDE SEQUENCE.
STRAIN=Clone pNL4-3;
Buckler C.E., Buckler-White A.J., Willey R.L., McCoy J.;
Submitted (JUN-1988) to the EMBL/GenBank/DDBJ databases.
[3]
PROTEIN SEQUENCE OF 56-68, AND CLEAVAGE BY VIRAL PROTEASE.
PubMed=7835426; DOI=10.1016/0014-5793(94)01370-G;
Gaedigk-Nitschko K., Schoen A., Wachinger G., Erfle V., Kohleisen B.;
"Cleavage of recombinant and cell derived human immunodeficiency virus
1 (HIV-1) Nef protein by HIV-1 protease.";
FEBS Lett. 357:275-278(1995).
[4]
MYRISTOYLATION AT GLY-2, FUNCTION IN VIRULENCE, AND MUTAGENESIS OF
2-GLY-GLY-3.
STRAIN=Clone pNL4-3;
PubMed=8151761;
Chowers M.Y., Spina C.A., Kwoh T.J., Fitch N.J.S., Richman D.D.,
Guatelli J.C.;
"Optimal infectivity in vitro of human immunodeficiency virus type 1
requires an intact nef gene.";
J. Virol. 68:2906-2914(1994).
[5]
FUNCTION, AND DI-LEUCINE MOTIF.
PubMed=8124721; DOI=10.1016/0092-8674(94)90360-3;
Aiken C., Konner J., Landau N.R., Lenburg M.E., Trono D.;
"Nef induces CD4 endocytosis: requirement for a critical dileucine
motif in the membrane-proximal CD4 cytoplasmic domain.";
Cell 76:853-864(1994).
[6]
SH3-BINDING REGION, AND MUTAGENESIS OF PRO-72; PRO-75; PRO-147 AND
PRO-150.
PubMed=7859737;
Saksela K., Cheng G., Baltimore D.;
"Proline-rich (PxxP) motifs in HIV-1 Nef bind to SH3 domains of a
subset of Src kinases and are required for the enhanced growth of Nef+
viruses but not for down-regulation of CD4.";
EMBO J. 14:484-491(1995).
[7]
INTERACTION WITH HUMAN LCK AND HUMAN MAPK3.
PubMed=8794306;
Greenway A.L., Azad A., Mills J., McPhee D.A.;
"Human immunodeficiency virus type 1 Nef binds directly to LCK and
mitogen-activated protein kinase, inhibiting kinase activity.";
J. Virol. 70:6701-6708(1996).
[8]
SUBCELLULAR LOCATION, AND CLEAVAGE BY VIRAL PROTEASE.
STRAIN=Clone pNL4-3;
PubMed=8623533; DOI=10.1006/viro.1996.0240;
Welker R., Kottler H., Kalbitzer H.R., Kraeusslich H.-G.;
"Human immunodeficiency virus type 1 Nef protein is incorporated into
virus particles and specifically cleaved by the viral proteinase.";
Virology 219:228-236(1996).
[9]
SUBCELLULAR LOCATION, AND N-TERMINAL DOMAIN.
STRAIN=Clone pNL4-3;
PubMed=9765428;
Welker R., Harris M., Cardel B., Kraeusslich H.-G.;
"Virion incorporation of human immunodeficiency virus type 1 Nef is
mediated by a bipartite membrane-targeting signal: analysis of its
role in enhancement of viral infectivity.";
J. Virol. 72:8833-8840(1998).
[10]
FUNCTION, AND MUTAGENESIS OF MET-20.
STRAIN=clone pNL-432;
PubMed=10684310; DOI=10.1128/JVI.74.6.2907-2912.2000;
Akari H., Arold S., Fukumori T., Okazaki T., Strebel K., Adachi A.;
"Nef-induced major histocompatibility complex class I down-regulation
is functionally dissociated from its virion incorporation, enhancement
of viral infectivity, and CD4 down-regulation.";
J. Virol. 74:2907-2912(2000).
[11]
FUNCTION, AND INTERACTION WITH HUMAN PAK2.
PubMed=11070003; DOI=10.1128/JVI.74.23.11081-11087.2000;
Arora V.K., Molina R.P., Foster J.L., Blakemore J.L., Chernoff J.,
Fredericksen B.L., Garcia J.V.;
"Lentivirus Nef specifically activates Pak2.";
J. Virol. 74:11081-11087(2000).
[12]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=11285224; DOI=10.1093/emboj/20.7.1593;
Swigut T., Shohdy N., Skowronski J.;
"Mechanism for down-regulation of CD28 by Nef.";
EMBO J. 20:1593-1604(2001).
[13]
FUNCTION, AND INTERACTION WITH HUMAN MAP3K5.
PubMed=11298454; DOI=10.1038/35071111;
Geleziunas R., Xu W., Takeda K., Ichijo H., Greene W.C.;
"HIV-1 Nef inhibits ASK1-dependent death signalling providing a
potential mechanism for protecting the infected host cell.";
Nature 410:834-838(2001).
[14]
MUTAGENESIS OF THR-71.
STRAIN=Clone pNL4-3;
PubMed=11525746; DOI=10.1016/S0960-9822(01)00373-6;
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.;
"A natural variability in the proline-rich motif of Nef modulates HIV-
1 replication in primary T cells.";
Curr. Biol. 11:1294-1299(2001).
[15]
FUNCTION, AND INTERACTION WITH HOST TP53.
STRAIN=Clone pNL4-3;
PubMed=11861836; DOI=10.1128/JVI.76.6.2692-2702.2002;
Greenway A.L., McPhee D.A., Allen K., Johnstone R., Holloway G.,
Mills J., Azad A., Sankovich S., Lambert P.;
"Human immunodeficiency virus type 1 Nef binds to tumor suppressor p53
and protects cells against p53-mediated apoptosis.";
J. Virol. 76:2692-2702(2002).
[16]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=14990729; DOI=10.1128/JVI.78.6.3099-3109.2004;
James C.O., Huang M.B., Khan M., Garcia-Barrio M., Powell M.D.,
Bond V.C.;
"Extracellular Nef protein targets CD4+ T cells for apoptosis by
interacting with CXCR4 surface receptors.";
J. Virol. 78:3099-3109(2004).
[17]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=14617802; DOI=10.1091/mbc.E03-08-0578;
Larsen J.E., Massol R.H., Nieland T.J.F., Kirchhausen T.;
"HIV Nef-mediated major histocompatibility complex class I down-
modulation is independent of Arf6 activity.";
Mol. Biol. Cell 15:323-331(2004).
[18]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=15854903; DOI=10.1016/j.cub.2005.02.058;
Michel N., Allespach I., Venzke S., Fackler O.T., Keppler O.T.;
"The Nef protein of human immunodeficiency virus establishes
superinfection immunity by a dual strategy to downregulate cell-
surface CCR5 and CD4.";
Curr. Biol. 15:714-723(2005).
[19]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=16928758; DOI=10.1128/JVI.01556-06;
Venzke S., Michel N., Allespach I., Fackler O.T., Keppler O.T.;
"Expression of Nef downregulates CXCR4, the major coreceptor of human
immunodeficiency virus, from the surfaces of target cells and thereby
enhances resistance to superinfection.";
J. Virol. 80:11141-11152(2006).
[20]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=18005690; DOI=10.1016/j.chom.2007.03.004;
Hung C.H., Thomas L., Ruby C.E., Atkins K.M., Morris N.P.,
Knight Z.A., Scholz I., Barklis E., Weinberg A.D., Shokat K.M.,
Thomas G.;
"HIV-1 Nef assembles a Src family kinase-ZAP-70/Syk-PI3K cascade to
downregulate cell-surface MHC-I.";
Cell Host Microbe 1:121-133(2007).
[21]
DIACIDIC MOTIF, MUTAGENESIS OF 164-LEU-LEU-165 AND 174-ASP-ASP-175,
AND INTERACTION WITH HOST AP-2 COMPLEX.
PubMed=18032517; DOI=10.1128/JVI.01874-07;
Lindwasser O.W., Smith W.J., Chaudhuri R., Yang P., Hurley J.H.,
Bonifacino J.S.;
"A diacidic motif in human immunodeficiency virus type 1 Nef is a
novel determinant of binding to AP-2.";
J. Virol. 82:1166-1174(2008).
[22]
IDENTIFICATION IN A CD4-NEF-AP2 COMPLEX.
STRAIN=Clone pNL4-3;
PubMed=19129443; DOI=10.1128/JVI.02227-08;
Chaudhuri R., Mattera R., Lindwasser O.W., Robinson M.S.,
Bonifacino J.S.;
"A basic patch on alpha-adaptin is required for binding of human
immunodeficiency virus type 1 Nef and cooperative assembly of a CD4-
Nef-AP-2 complex.";
J. Virol. 83:2518-2530(2009).
[23]
REVIEW.
PubMed=25585010; DOI=10.1016/j.bbagen.2015.01.003;
Pawlak E.N., Dikeakos J.D.;
"HIV-1 Nef: a master manipulator of the membrane trafficking machinery
mediating immune evasion.";
Biochim. Biophys. Acta 1850:733-741(2015).
[24]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=26416734; DOI=10.1038/nature15399;
Rosa A., Chande A., Ziglio S., De Sanctis V., Bertorelli R., Goh S.L.,
McCauley S.M., Nowosielska A., Antonarakis S.E., Luban J.,
Santoni F.A., Pizzato M.;
"HIV-1 Nef promotes infection by excluding SERINC5 from virion
incorporation.";
Nature 526:212-217(2015).
[25]
FUNCTION.
STRAIN=Clone pNL4-3;
PubMed=26416733; DOI=10.1038/nature15400;
Usami Y., Wu Y., Goettlinger H.G.;
"SERINC3 and SERINC5 restrict HIV-1 infectivity and are counteracted
by Nef.";
Nature 526:218-223(2015).
[26]
SUBUNIT, AND SUBCELLULAR LOCATION.
STRAIN=Clone pNL4-3;
PubMed=19781555; DOI=10.1016/j.jmb.2009.09.047;
Poe J.A., Smithgall T.E.;
"HIV-1 Nef dimerization is required for Nef-mediated receptor down-
regulation and viral replication.";
J. Mol. Biol. 394:329-342(2009).
[27]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 54-205 IN COMPLEX WITH A SRC
FAMILY SH3 DOMAIN.
PubMed=8681387; DOI=10.1016/S0092-8674(00)81276-3;
Lee C.H., Saksela K., Mirza U.A., Chait B.T., Kuriyan J.;
"Crystal structure of the conserved core of HIV-1 Nef complexed with a
Src family SH3 domain.";
Cell 85:931-942(1996).
-!- FUNCTION: Factor of infectivity and pathogenicity, required for
optimal virus replication (PubMed:8151761). Alters numerous
pathways of T-lymphocytes function and down-regulates immunity
surface molecules in order to evade host defense and increase
viral infectivity (PubMed:25585010). Alters the functionality of
other immunity cells, like dendritic cells, monocytes/macrophages
and NK cells (PubMed:25585010). {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:25585010, ECO:0000269|PubMed:8151761}.
-!- FUNCTION: 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). 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.
{ECO:0000255|HAMAP-Rule:MF_04078, ECO:0000269|PubMed:10684310,
ECO:0000269|PubMed:11285224, ECO:0000269|PubMed:14617802,
ECO:0000269|PubMed:15854903, ECO:0000269|PubMed:16928758,
ECO:0000269|PubMed:18005690, ECO:0000269|PubMed:26416733,
ECO:0000269|PubMed:26416734}.
-!- FUNCTION: 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) (By similarity). Increasing surface FasL molecules
and decreasing surface MHC-I molecules on infected CD4(+) cells
send attacking cytotoxic CD8+ T-lymphocytes into apoptosis
(PubMed:11298454). {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:11298454}.
-!- FUNCTION: 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.
Decreases the half-life of TP53, 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 host BAD. {ECO:0000255|HAMAP-
Rule:MF_04078, ECO:0000269|PubMed:11298454,
ECO:0000269|PubMed:11861836}.
-!- FUNCTION: Extracellular Nef protein targets CD4(+) T-lymphocytes
for apoptosis by interacting with CXCR4 surface receptors
(PubMed:14990729). {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:14990729}.
-!- SUBUNIT: Monomer; cytosolic form. Homodimer; membrane bound form.
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. 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 host AP2 subunit alpha and
AP2 subunit sigma2. Interacts with TCR-zeta chain; this
interaction up-regulates the Fas ligand (FasL) surface expression.
Interacts with host HCK, LYN, and SRC; these interactions activate
the Src family kinases. Interacts with MAP3K5; this interaction
inhibits the Fas and TNFR-mediated death signals. Interacts with
beta-COP and PTE1. Interacts with human RACK1; this increases Nef
phosphorylation by PKC. Interacts with TP53; this interaction
decreases the half-life of TP53, protecting the infected cell
against p53-mediated apoptosis. {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:11070003, ECO:0000269|PubMed:11298454,
ECO:0000269|PubMed:11861836, ECO:0000269|PubMed:18032517,
ECO:0000269|PubMed:19781555, ECO:0000269|PubMed:8794306}.
-!- INTERACTION:
P08631:HCK (xeno); NbExp=2; IntAct=EBI-15672419, EBI-346340;
-!- SUBCELLULAR LOCATION: Host cell membrane {ECO:0000255|HAMAP-
Rule:MF_04078, ECO:0000269|PubMed:19781555}; Lipid-anchor
{ECO:0000255|HAMAP-Rule:MF_04078, ECO:0000269|PubMed:19781555};
Cytoplasmic side {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:19781555}. Virion {ECO:0000255|HAMAP-
Rule:MF_04078, ECO:0000269|PubMed:8623533,
ECO:0000269|PubMed:9765428}. Secreted {ECO:0000255|HAMAP-
Rule:MF_04078}. Host Golgi apparatus membrane {ECO:0000255|HAMAP-
Rule:MF_04078, ECO:0000269|PubMed:19781555}. 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. {ECO:0000255|HAMAP-
Rule:MF_04078, ECO:0000269|PubMed:19781555,
ECO:0000269|PubMed:8623533, ECO:0000269|PubMed:9765428}.
-!- INDUCTION: Expressed early in the viral replication cycle.
{ECO:0000255|HAMAP-Rule:MF_04078}.
-!- 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 TP53. {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:11861836, ECO:0000269|PubMed:8151761}.
-!- DOMAIN: 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.
{ECO:0000255|HAMAP-Rule:MF_04078, ECO:0000269|PubMed:7859737,
ECO:0000269|PubMed:8681387}.
-!- DOMAIN: The dileucine internalization motif and a diacidic motif
seem to be required for binding to AP-2. {ECO:0000255|HAMAP-
Rule:MF_04078, ECO:0000269|PubMed:18032517}.
-!- DOMAIN: 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. {ECO:0000255|HAMAP-
Rule:MF_04078}.
-!- PTM: 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. {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:7835426, ECO:0000269|PubMed:8623533}.
-!- PTM: Myristoylated. {ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:8151761}.
-!- PTM: Phosphorylated on serine residues, probably by host PKCdelta
and theta. {ECO:0000255|HAMAP-Rule:MF_04078}.
-!- MISCELLANEOUS: The infectious clone pNL4-3 is a chimeric provirus
that consists of DNA from HIV isolates NY5 (5' half) and BRU (3'
half).
-!- 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). {ECO:0000255|HAMAP-Rule:MF_04078}.
-!- SIMILARITY: Belongs to the lentivirus primate group Nef protein
family. {ECO:0000255|HAMAP-Rule:MF_04078}.
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EMBL; K02013; AAB59752.1; -; Genomic_RNA.
EMBL; M19921; AAA44993.1; -; Genomic_RNA.
EMBL; A04321; CAA00353.1; -; Unassigned_RNA.
PIR; A04008; ASLJFV.
PDB; 1AVV; X-ray; 3.00 A; A=58-206.
PDB; 1AVZ; X-ray; 3.00 A; A/B=58-206.
PDB; 1EFN; X-ray; 2.50 A; B/D=54-205.
PDB; 4D8D; X-ray; 2.52 A; B/D=58-204.
PDBsum; 1AVV; -.
PDBsum; 1AVZ; -.
PDBsum; 1EFN; -.
PDBsum; 4D8D; -.
DisProt; DP00048; -.
ProteinModelPortal; P03406; -.
SMR; P03406; -.
DIP; DIP-29968N; -.
ELM; P03406; -.
IntAct; P03406; 1.
BindingDB; P03406; -.
OrthoDB; VOG090000RB; -.
EvolutionaryTrace; P03406; -.
Proteomes; UP000007692; Genome.
GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
GO; GO:0044178; C:host cell Golgi membrane; IEA:UniProtKB-SubCell.
GO; GO:0020002; C:host cell plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
GO; GO:0019012; C:virion; IEA:UniProtKB-SubCell.
GO; GO:0051117; F:ATPase binding; IPI:UniProtKB.
GO; GO:0005516; F:calmodulin binding; IPI:UniProtKB.
GO; GO:0042609; F:CD4 receptor binding; IPI:UniProtKB.
GO; GO:0005525; F:GTP binding; IEA:InterPro.
GO; GO:0042288; F:MHC class I protein binding; IPI:UniProtKB.
GO; GO:0019901; F:protein kinase binding; IPI:UniProtKB.
GO; GO:0005102; F:receptor binding; IPI:UniProtKB.
GO; GO:0017124; F:SH3 domain binding; IPI:UniProtKB.
GO; GO:0031996; F:thioesterase binding; IPI:UniProtKB.
GO; GO:0052085; P:negative regulation by symbiont of host T-cell mediated immune response; IDA:UniProtKB.
GO; GO:0045225; P:negative regulation of CD4 biosynthetic process; IDA:UniProtKB.
GO; GO:0009405; P:pathogenesis; IDA:UniProtKB.
GO; GO:0043946; P:positive regulation of catalytic activity in other organism involved in symbiotic interaction; IDA:UniProtKB.
GO; GO:0050848; P:regulation of calcium-mediated signaling; IDA:UniProtKB.
GO; GO:0050863; P:regulation of T cell activation; NAS:UniProtKB.
GO; GO:0039504; P:suppression by virus of host adaptive immune response; IEA:UniProtKB-KW.
GO; GO:0046776; P:suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I; IDA:UniProtKB.
GO; GO:0039505; P:suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II; IEA:UniProtKB-KW.
GO; GO:0039521; P:suppression by virus of host autophagy; IEA:UniProtKB-KW.
GO; GO:0019058; P:viral life cycle; IDA:UniProtKB.
Gene3D; 3.30.62.10; -; 1.
Gene3D; 4.10.890.10; -; 1.
HAMAP; MF_04078; NEF_HIV; 1.
InterPro; IPR027480; HIV-1_Nef_anchor.
InterPro; IPR027481; HIV-1_Nef_core.
InterPro; IPR001558; HIV_Nef.
Pfam; PF00469; F-protein; 1.
SUPFAM; SSF55671; SSF55671; 1.
1: Evidence at protein level;
3D-structure; AIDS; Apoptosis; Complete proteome;
Direct protein sequencing; Early protein; Host cell membrane;
Host Golgi apparatus; Host membrane; 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;
Lipoprotein; Membrane; Myristate; Phosphoprotein; Secreted;
SH3-binding; Viral immunoevasion; Virion; Virulence.
INIT_MET 1 1 Removed; by host. {ECO:0000255|HAMAP-
Rule:MF_04078}.
CHAIN 2 206 Protein Nef. {ECO:0000255|HAMAP-
Rule:MF_04078}.
/FTId=PRO_0000038335.
CHAIN 58 206 C-terminal core protein.
{ECO:0000255|HAMAP-Rule:MF_04078}.
/FTId=PRO_0000038336.
REGION 62 65 Acidic; interacts with host PACS1 and
PACS2; stabilizes the interaction of
NEF/MHC-I with host AP1M1; necessary for
MHC-I internalization.
{ECO:0000255|HAMAP-Rule:MF_04078}.
REGION 69 78 SH3-binding; interaction with Src family
tyrosine kinases. {ECO:0000255|HAMAP-
Rule:MF_04078,
ECO:0000269|PubMed:7859737,
ECO:0000269|PubMed:8681387}.
REGION 108 124 Mediates dimerization, Nef-PTE1
interaction. {ECO:0000255|HAMAP-
Rule:MF_04078}.
REGION 108 124 Mediates dimerization, Nef-PTE1
interaction, Nef-induced CD4 and MHC-I
down-regulation and enhancement of
infectivity.
{ECO:0000269|PubMed:19781555}.
REGION 148 180 Binding to ATP6V1H. {ECO:0000255|HAMAP-
Rule:MF_04078}.
MOTIF 72 75 PxxP; stabilizes the interaction of
NEF/MHC-I with host AP1M1; necessary for
MHC-I internalization.
{ECO:0000255|HAMAP-Rule:MF_04078}.
MOTIF 164 165 Dileucine internalization motif;
necessary for CD4 internalization.
{ECO:0000255|HAMAP-Rule:MF_04078}.
MOTIF 174 175 Diacidic; necessary for CD4
internalization. {ECO:0000255|HAMAP-
Rule:MF_04078,
ECO:0000269|PubMed:18032517}.
SITE 20 20 Might play a role in AP-1 recruitment to
the Nef-MHC-I complex.
{ECO:0000255|HAMAP-Rule:MF_04078}.
SITE 57 58 Cleavage; by viral protease.
{ECO:0000255|HAMAP-Rule:MF_04078,
ECO:0000269|PubMed:7835426}.
MOD_RES 6 6 Phosphoserine; by host.
{ECO:0000255|HAMAP-Rule:MF_04078}.
LIPID 2 2 N-myristoyl glycine; by host.
{ECO:0000255|HAMAP-Rule:MF_04078}.
VARIANT 11 11 V -> I (in strain: Clone pNL4-3).
VARIANT 15 15 T -> A (in strain: Clone pNL4-3).
VARIANT 33 33 A -> V (in strain: Clone pNL4-3).
VARIANT 51 51 T -> N (in strain: Clone pNL4-3).
MUTAGEN 2 3 GG->AA: 70% loss of infectivity.
{ECO:0000269|PubMed:8151761}.
MUTAGEN 20 20 M->A: Amost complete loss of Nef-induced
MHC-I down-regulation.
{ECO:0000269|PubMed:10684310}.
MUTAGEN 20 20 M->R: Amost complete loss of Nef-induced
MHC-I down-regulation.
{ECO:0000269|PubMed:10684310}.
MUTAGEN 71 71 T->R: Increases infectivity by a factor
of three. {ECO:0000269|PubMed:11525746}.
MUTAGEN 72 72 P->A: Complete loss of binding to HCK SH3
domain and altered viral growth; when
associated with P-76. No effect on Nef-
induced CD4 down-regulation.
{ECO:0000269|PubMed:7859737}.
MUTAGEN 75 75 P->A: Complete loss of binding to HCK SH3
domain and altered viral growth; when
associated with P-73. No effect on Nef-
induced CD4 down-regulation.
{ECO:0000269|PubMed:7859737}.
MUTAGEN 147 147 P->A: Complete loss of binding to HCK SH3
domain and altered viral growth. No
effect on Nef-induced CD4 down-
modulation. {ECO:0000269|PubMed:7859737}.
MUTAGEN 150 150 P->A: No effect.
{ECO:0000269|PubMed:7859737}.
MUTAGEN 164 165 LL->AA: Loss of interaction with AP-2
complex. {ECO:0000269|PubMed:18032517}.
MUTAGEN 174 175 DD->AA: Loss of interaction with AP-2
complex. {ECO:0000269|PubMed:18032517}.
HELIX 81 93 {ECO:0000244|PDB:1EFN}.
TURN 97 99 {ECO:0000244|PDB:1AVZ}.
HELIX 104 118 {ECO:0000244|PDB:1EFN}.
STRAND 130 132 {ECO:0000244|PDB:1EFN}.
STRAND 136 138 {ECO:0000244|PDB:1EFN}.
STRAND 143 147 {ECO:0000244|PDB:1EFN}.
STRAND 181 185 {ECO:0000244|PDB:1EFN}.
HELIX 187 190 {ECO:0000244|PDB:1EFN}.
HELIX 194 198 {ECO:0000244|PDB:1EFN}.
HELIX 200 202 {ECO:0000244|PDB:1EFN}.
SEQUENCE 206 AA; 23342 MW; 77453FC80B6004F2 CRC64;
MGGKWSKSSV VGWPTVRERM RRAEPAADGV GAASRDLEKH GAITSSNTAA TNAACAWLEA
QEEEEVGFPV TPQVPLRPMT YKAAVDLSHF LKEKGGLEGL IHSQRRQDIL DLWIYHTQGY
FPDWQNYTPG PGVRYPLTFG WCYKLVPVEP DKVEEANKGE NTSLLHPVSL HGMDDPEREV
LEWRFDSRLA FHHVARELHP EYFKNC


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