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Nef protein

 Q9Q6V7_9HIV1            Unreviewed;       202 AA.
Q9Q6V7;
01-MAY-2000, integrated into UniProtKB/TrEMBL.
01-MAY-2000, sequence version 1.
05-DEC-2018, entry version 89.
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:AAF22322.1};
HIV-1 CRF03_AB.
Viruses; Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus.
NCBI_TaxID=540995 {ECO:0000313|EMBL:AAF22322.1, ECO:0000313|Proteomes:UP000107373};
[1] {ECO:0000313|EMBL:AAF22322.1, ECO:0000313|Proteomes:UP000107373}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=KAL153 {ECO:0000313|EMBL:AAF22322.1};
PubMed=10933619; DOI=10.1089/08892220050075309;
Liitsola K., Holm K., Bobkov A., Pokrovsky V., Smolskaya T.,
Leinikki P., Osmanov S., Salminen M.;
"An AB recombinant and its parental HIV type 1 strains in the area of
the former Soviet Union: low requirements for sequence identity in
recombination. UNAIDS Virus Isolation Network.";
AIDS Res. Hum. Retroviruses 16:1047-1053(2000).
-!- 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; AF193276; AAF22322.1; -; Genomic_DNA.
ProteinModelPortal; Q9Q6V7; -.
Proteomes; UP000107373; 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-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};
Complete proteome {ECO:0000313|Proteomes:UP000107373};
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 1 Removed; by host. {ECO:0000256|HAMAP-
Rule:MF_04078}.
REGION 63 66 Acidic; interacts with host PACS1 and
PACS2; stabilizes the interaction of
NEF/MHC-I with host AP1M1; necessary for
MHC-I internalization.
{ECO:0000256|HAMAP-Rule:MF_04078}.
REGION 70 79 SH3-binding; interaction with Src family
tyrosine kinases. {ECO:0000256|HAMAP-
Rule:MF_04078}.
REGION 109 125 Mediates dimerization, Nef-PTE1
interaction. {ECO:0000256|HAMAP-
Rule:MF_04078}.
REGION 144 176 Binding to ATP6V1H. {ECO:0000256|HAMAP-
Rule:MF_04078}.
MOTIF 73 76 PxxP; stabilizes the interaction of
NEF/MHC-I with host AP1M1; necessary for
MHC-I internalization.
{ECO:0000256|HAMAP-Rule:MF_04078}.
MOTIF 160 161 Dileucine internalization motif;
necessary for CD4 internalization.
{ECO:0000256|HAMAP-Rule:MF_04078}.
MOTIF 170 171 Diacidic; necessary for CD4
internalization. {ECO:0000256|HAMAP-
Rule:MF_04078}.
SITE 58 59 Cleavage; by viral protease.
{ECO:0000256|HAMAP-Rule:MF_04078}.
MOD_RES 6 6 Phosphoserine; by host.
{ECO:0000256|HAMAP-Rule:MF_04078}.
LIPID 2 2 N-myristoyl glycine; by host.
{ECO:0000256|HAMAP-Rule:MF_04078}.
SEQUENCE 202 AA; 23020 MW; 3B9EFBA099C97D93 CRC64;
MGGKWSKSSI VGWPQVRERI RRAPAPAARG VGPVSQDLDK YGAVTSSNTA ANNADCAWLE
AQEEEEVGFP VRPQVPLRPM TYKGAFDLSH FLKEKGGLDG LIYSKKRQEI LDLWVYHTQG
YFPDWQPGIR FPLTFGWCYK LVPVDPAEVE EATEGENNSL LHPICQHGMD DEEKEVLMWK
FDSRLALTHR ARELHPEFYK DC


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