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

 NEF_HV1LA               Reviewed;         202 AA.
Q9QPN3;
13-SEP-2004, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
25-OCT-2017, entry version 107.
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};
Flags: Fragment;
Name=nef {ECO:0000255|HAMAP-Rule:MF_04078};
Human immunodeficiency virus type 1 group M subtype B (isolate Lai)
(HIV-1).
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae;
Lentivirus; Primate lentivirus group.
NCBI_TaxID=290579;
NCBI_TaxID=9606; Homo sapiens (Human).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Piedade J., Esteves A., Parreira R., Venenno T., Barros M.F.,
Canas-Ferreira W.F.;
Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases.
[2]
INTERACTION WITH HUMAN BETA-COP.
PubMed=7982906;
Benichou S., Bomsel M., Bodeus M., Durand H., Doute M., Letourneur F.,
Camonis J., Benarous R.;
"Physical interaction of the HIV-1 Nef protein with beta-COP, a
component of non-clathrin-coated vesicles essential for membrane
traffic.";
J. Biol. Chem. 269:30073-30076(1994).
[3]
INTERACTION WITH HUMAN PTE1, AND MUTANT NEF*4.
PubMed=9153233; DOI=10.1074/jbc.272.21.13779;
Liu L.X., Margottin F., Le Gall S., Schwartz O., Selig L.,
Benarous R., Benichou S.;
"Binding of HIV-1 Nef to a novel thioesterase enzyme correlates with
Nef-mediated CD4 down-regulation.";
J. Biol. Chem. 272:13779-13785(1997).
[4]
FUNCTION, HOMODIMERIZATION, AND MUTAGENESIS OF TRP-57; ASP-108;
ASP-111; LEU-112; PHE-121; PRO-122; ASP-123; TRP-124 AND ASN-126.
PubMed=10799608; DOI=10.1128/JVI.74.11.5310-5319.2000;
Liu L.X., Heveker N., Fackler O.T., Arold S., Le Gall S., Janvier K.,
Peterlin B.M., Dumas C., Schwartz O., Benichou S., Benarous R.;
"Mutation of a conserved residue (D123) required for oligomerization
of human immunodeficiency virus type 1 Nef protein abolishes
interaction with human thioesterase and results in impairment of Nef
biological functions.";
J. Virol. 74:5310-5319(2000).
[5]
FUNCTION, AND MUTAGENESIS OF 154-GLU-GLU-155; 164-LEU-LEU-165 AND
174-ASP-ASP-175.
PubMed=11264386; DOI=10.1128/JVI.75.8.3971-3976.2001;
Janvier K., Craig H., Le Gall S., Benarous R., Guatelli J.,
Schwartz O., Benichou S.;
"Nef-induced CD4 down-regulation: a diacidic sequence in human
immunodeficiency virus type 1 Nef does not function as a protein
sorting motif through direct binding to beta-COP.";
J. Virol. 75:3971-3976(2001).
-!- 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:0000255|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:0000255|HAMAP-Rule:MF_04078}.
-!- 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:0000255|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:0000255|HAMAP-
Rule:MF_04078}.
-!- FUNCTION: Extracellular Nef protein targets CD4(+) T-lymphocytes
for apoptosis by interacting with CXCR4 surface receptors.
{ECO:0000255|HAMAP-Rule:MF_04078}.
-!- 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}.
-!- INTERACTION:
P50570:DNM2 (xeno); NbExp=4; IntAct=EBI-7355146, EBI-346547;
-!- SUBCELLULAR LOCATION: Host cell membrane {ECO:0000255|HAMAP-
Rule:MF_04078}; Lipid-anchor {ECO:0000255|HAMAP-Rule:MF_04078};
Cytoplasmic side {ECO:0000255|HAMAP-Rule:MF_04078}. Virion
{ECO:0000255|HAMAP-Rule:MF_04078}. Secreted {ECO:0000255|HAMAP-
Rule:MF_04078}. Host Golgi apparatus membrane {ECO:0000255|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:0000255|HAMAP-Rule:MF_04078}.
-!- 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}.
-!- 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}.
-!- DOMAIN: The dileucine internalization motif and a diacidic motif
seem to be required for binding to AP-2. {ECO:0000255|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: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}.
-!- PTM: Myristoylated. {ECO:0000255|HAMAP-Rule:MF_04078}.
-!- PTM: Phosphorylated on serine residues, probably by host PKCdelta
and theta. {ECO:0000255|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: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; AF166101; AAD47831.1; -; Genomic_DNA.
ProteinModelPortal; Q9QPN3; -.
SMR; Q9QPN3; -.
DIP; DIP-45114N; -.
IntAct; Q9QPN3; 1.
MINT; MINT-1206736; -.
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:0005525; F:GTP binding; IEA:InterPro.
GO; GO:0017124; F:SH3 domain binding; IEA:UniProtKB-KW.
GO; GO:0009405; P:pathogenesis; IEA:UniProtKB-KW.
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; IEA:UniProtKB-KW.
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.
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;
AIDS; Apoptosis; 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 2 202 Protein Nef. {ECO:0000255|HAMAP-
Rule:MF_04078}.
/FTId=PRO_0000038323.
CHAIN 58 202 C-terminal core protein.
{ECO:0000255|HAMAP-Rule:MF_04078}.
/FTId=PRO_0000038324.
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}.
REGION 108 124 Mediates dimerization, Nef-PTE1
interaction. {ECO:0000255|HAMAP-
Rule:MF_04078}.
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}.
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}.
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}.
MUTAGEN 57 57 W->R: In Nef*4; complete loss of Nef-
induced CD4 down-regulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 68 68 F->S: In Nef*4.
MUTAGEN 108 108 D->A: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 111 111 D->G: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 112 112 L->D: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 121 121 F->G: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 122 122 P->R: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 123 123 D->G: In Nef*4; complete loss of Nef-PTE1
interaction, Nef-induced CD4 and MHC-I
down-regulation and enhancement of
infectivity.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 123 123 D->V: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 124 124 W->R: Complete loss of Nef-PTE1
interaction and Nef-induced CD4 down-
modulation.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 126 126 N->S: No effect.
{ECO:0000269|PubMed:10799608}.
MUTAGEN 154 155 EE->GG: No effect on beta-COP
interaction.
{ECO:0000269|PubMed:11264386}.
MUTAGEN 164 165 LL->AA: Complete loss of CD4 down-
modulation; no effect on beta-COP
interaction.
{ECO:0000269|PubMed:11264386}.
MUTAGEN 166 166 H->R: In Nef*4.
MUTAGEN 170 170 L->Q: In Nef*4.
MUTAGEN 174 175 DD->AA: Complete loss of CD4 down-
modulation; no effect on beta-COP
interaction.
{ECO:0000269|PubMed:11264386}.
NON_TER 202 202
SEQUENCE 202 AA; 23033 MW; CD61DFA6F386CC89 CRC64;
MGGKWSKSSV VGWPAVRERM RRAEPAADGV GAVSRDLEKH GAITSSNTAA TNADCAWLEA
QEEEEVGFPV TPQVPLRPMT YKAAVDLSHF LKEKGGLEGL IHSQRRQDIL DLWIYHTQGY
FPDWQNYTPE PGVRYPLTFG WCYKLVPVEP DKVEEANKGE NTRLLHPVSL HGMDDPEREV
LEWRFDSRLA FHHVARELHP EY


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