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

 A0A410SW27_9HIV1        Unreviewed;       213 AA.
A0A410SW27;
08-MAY-2019, integrated into UniProtKB/TrEMBL.
08-MAY-2019, sequence version 1.
11-DEC-2019, entry version 4.
RecName: Full=Protein Nef {ECO:0000256|HAMAP-Rule:MF_04078};
AltName: Full=3'ORF {ECO:0000256|HAMAP-Rule:MF_04078};
AltName: Full=Negative factor {ECO:0000256|HAMAP-Rule:MF_04078};
Short=F-protein {ECO:0000256|HAMAP-Rule:MF_04078};
Contains:
RecName: Full=C-terminal core protein {ECO:0000256|HAMAP-Rule:MF_04078};
Name=nef {ECO:0000256|HAMAP-Rule:MF_04078, ECO:0000313|EMBL:QAU00534.1};
Human immunodeficiency virus 1.
Viruses; Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
NCBI_TaxID=11676 {ECO:0000313|EMBL:QAU00534.1};
NCBI_TaxID=9606; Homo sapiens (Human).
[1] {ECO:0000313|EMBL:QAU00534.1}
NUCLEOTIDE SEQUENCE.
STRAIN=9243_W12_9G13_S35 {ECO:0000313|EMBL:QAU00534.1};
PubMed=30420517; DOI=10.1073/pnas.1813512115;
Lu C.L., Pai J.A., Nogueira L., Mendoza P., Gruell H., Oliveira T.Y.,
Barton J., Lorenzi J.C., Cohen Y.Z., Cohn L.B., Klein F., Caskey M.,
Nussenzweig M.C., Jankovic M.;
"Relationship between intact HIV-1 proviruses in circulating CD4+ T cells
and rebound viruses emerging during treatment interruption.";
Proc. Natl. Acad. Sci. U.S.A. 115:E11341-E11348(2018).
[2] {ECO:0000313|EMBL:QAU00534.1}
NUCLEOTIDE SEQUENCE.
STRAIN=9243_W12_9G13_S35 {ECO:0000313|EMBL:QAU00534.1};
Lu C.-L., Pai J., Nogueira L., Mendoza P., Gruell H., Oliveira T.,
Barton J., Lorenzi J., Cohen Y., Cohn L., Klein F., Caskey M.,
Nussenzweig M., Jankovic M.;
Submitted (OCT-2018) to the EMBL/GenBank/DDBJ databases.
-!- 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).
Increasing surface FasL molecules and decreasing surface MHC-I
molecules on infected CD4(+) cells send attacking cytotoxic CD8+ T-
lymphocytes into apoptosis. {ECO:0000256|HAMAP-Rule:MF_04078}.
-!- FUNCTION: Extracellular Nef protein targets CD4(+) T-lymphocytes for
apoptosis by interacting with CXCR4 surface receptors.
{ECO:0000256|HAMAP-Rule:MF_04078}.
-!- 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. {ECO:0000256|HAMAP-Rule:MF_04078}.
-!- 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:0000256|HAMAP-Rule:MF_04078}.
-!- 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:0000256|HAMAP-Rule:MF_04078}.
-!- SUBUNIT: Homodimer. {ECO:0000256|SAAS:SAAS01051624}.
-!- 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:0000256|HAMAP-Rule:MF_04078}.
-!- SUBCELLULAR LOCATION: Host cell membrane {ECO:0000256|HAMAP-
Rule:MF_04078}; Lipid-anchor {ECO:0000256|HAMAP-Rule:MF_04078};
Cytoplasmic side {ECO:0000256|HAMAP-Rule:MF_04078}. Virion
{ECO:0000256|HAMAP-Rule:MF_04078}. Secreted {ECO:0000256|HAMAP-
Rule:MF_04078}. Host Golgi apparatus membrane {ECO:0000256|HAMAP-
Rule:MF_04078}. 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:0000256|HAMAP-Rule:MF_04078}.
-!- INDUCTION: Expressed early in the viral replication cycle.
{ECO:0000256|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:0000256|HAMAP-Rule:MF_04078}.
-!- 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:0000256|HAMAP-Rule:MF_04078}.
-!- 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:0000256|HAMAP-Rule:MF_04078}.
-!- DOMAIN: The dileucine internalization motif and a diacidic motif seem
to be required for binding to AP-2. {ECO:0000256|HAMAP-Rule:MF_04078}.
-!- PTM: Myristoylated. {ECO:0000256|HAMAP-Rule:MF_04078}.
-!- PTM: Phosphorylated on serine residues, probably by host PKCdelta and
theta. {ECO:0000256|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:0000256|HAMAP-Rule:MF_04078}.
-!- 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:0000256|HAMAP-Rule:MF_04078}.
-!- SIMILARITY: Belongs to the lentivirus primate group Nef protein family.
{ECO:0000256|HAMAP-Rule:MF_04078, ECO:0000256|RuleBase:RU000344,
ECO:0000256|SAAS:SAAS01051605}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation of
feature annotation. {ECO:0000256|HAMAP-Rule:MF_04078}.
---------------------------------------------------------------------------
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EMBL; MK115134; QAU00534.1; -; Genomic_DNA.
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-UniRule.
GO; GO:0019012; C:virion; IEA:UniProtKB-SubCell.
GO; GO:0005525; F:GTP binding; IEA:UniProtKB-UniRule.
GO; GO:0017124; F:SH3 domain binding; IEA:UniProtKB-UniRule.
GO; GO:0009405; P:pathogenesis; IEA:UniProtKB-KW.
GO; GO:0039504; P:suppression by virus of host adaptive immune response; IEA:UniProtKB-UniRule.
GO; GO:0046776; P:suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I; IEA:UniProtKB-UniRule.
GO; GO:0039505; P:suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II; IEA:UniProtKB-UniRule.
GO; GO:0039521; P:suppression by virus of host autophagy; IEA:UniProtKB-UniRule.
Gene3D; 3.30.62.10; -; 1.
Gene3D; 4.10.890.10; -; 1.
HAMAP; MF_04078; NEF_HIV; 1.
InterPro; IPR027480; HIV-1_Nef_anchor_sf.
InterPro; IPR027481; HIV-1_Nef_core_sf.
InterPro; IPR001558; HIV_Nef.
Pfam; PF00469; F-protein; 1.
SUPFAM; SSF55671; SSF55671; 1.
2: Evidence at transcript level;
Apoptosis {ECO:0000256|HAMAP-Rule:MF_04078};
Early protein {ECO:0000256|HAMAP-Rule:MF_04078};
Host cell membrane {ECO:0000256|HAMAP-Rule:MF_04078,
ECO:0000256|SAAS:SAAS01051610};
Host Golgi apparatus {ECO:0000256|HAMAP-Rule:MF_04078};
Host membrane {ECO:0000256|HAMAP-Rule:MF_04078,
ECO:0000256|SAAS:SAAS01051610};
Host-virus interaction {ECO:0000256|HAMAP-Rule:MF_04078};
Inhibition of host adaptive immune response by virus {ECO:0000256|HAMAP-
Rule:MF_04078};
Inhibition of host autophagy by virus {ECO:0000256|HAMAP-Rule:MF_04078};
Inhibition of host MHC class I molecule presentation by virus
{ECO:0000256|HAMAP-Rule:MF_04078};
Inhibition of host MHC class II molecule presentation by virus
{ECO:0000256|HAMAP-Rule:MF_04078};
Lipoprotein {ECO:0000256|HAMAP-Rule:MF_04078,
ECO:0000256|RuleBase:RU000344};
Membrane {ECO:0000256|HAMAP-Rule:MF_04078, ECO:0000256|SAAS:SAAS01051610};
Myristate {ECO:0000256|HAMAP-Rule:MF_04078, ECO:0000256|RuleBase:RU000344};
Phosphoprotein {ECO:0000256|HAMAP-Rule:MF_04078};
Secreted {ECO:0000256|HAMAP-Rule:MF_04078};
SH3-binding {ECO:0000256|HAMAP-Rule:MF_04078};
Viral immunoevasion {ECO:0000256|HAMAP-Rule:MF_04078};
Virion {ECO:0000256|HAMAP-Rule:MF_04078};
Virulence {ECO:0000256|HAMAP-Rule:MF_04078, ECO:0000256|RuleBase:RU000344}.
INIT_MET 1
/note="Removed; by host"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
CHAIN 2..213
/note="Protein Nef"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
/id="PRO_5023407492"
CHAIN 64..213
/note="C-terminal core protein"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
/id="PRO_5023407493"
REGION 76..85
/note="SH3-binding; interaction with Src family tyrosine
kinases"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
REGION 115..131
/note="Mediates dimerization, Nef-PTE1 interaction"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
REGION 155..187
/note="Binding to ATP6V1H"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
MOTIF 79..82
/note="PxxP; stabilizes the interaction of NEF/MHC-I with
host AP1M1; necessary for MHC-I internalization"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
MOTIF 171..172
/note="Dileucine internalization motif; necessary for CD4
internalization"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
MOTIF 181..182
/note="Diacidic; necessary for CD4 internalization"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
SITE 20
/note="Might play a role in AP-1 recruitment to the Nef-
MHC-I complex"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
MOD_RES 6
/note="Phosphoserine; by host"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
LIPID 2
/note="N-myristoyl glycine; by host"
/evidence="ECO:0000256|HAMAP-Rule:MF_04078"
SEQUENCE 213 AA; 24199 MW; 0BEB4A824E5FE9F9 CRC64;
MGNKLSRGLR AGWPAIRERM RRARPVREPE PAAAGVGAAS RDLERHGALT SSNTAATNAD
VACLEAQQEE EEVGFPVRPQ VPLRPMTYKG ALDISHFLKE KGGLDGLIYS KRRQDILDLW
LYNTQGYFPD WQNYTPGPGV RFPLCFGWCF KLVPVDPDKV EEASVGENNC LLSPENLHGI
EDEHREVLQW RFDSRLAFHH VARELHPEYY KDC


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