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Protein

Protein Nef

Gene

nef

Organism
Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation1 Publication
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.UniRule annotation3 Publications
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.UniRule annotation
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 Bad.UniRule annotation
Extracellular Nef protein targets CD4+ T-lymphocytes for apoptosis by interacting with CXCR4 surface receptors.UniRule annotation1 Publication

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).UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei20Might play a role in AP-1 recruitment to the Nef-MHC-I complexUniRule annotation1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Biological processApoptosis, 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, Viral immunoevasion, Virulence

Enzyme and pathway databases

ReactomeiR-HSA-162585. Uncoating of the HIV Virion.
R-HSA-162588. Budding and maturation of HIV virion.
R-HSA-162599. Late Phase of HIV Life Cycle.
R-HSA-164939. Nef mediated downregulation of CD28 cell surface expression.
R-HSA-164940. Nef mediated downregulation of MHC class I complex cell surface expression.
R-HSA-164944. Nef and signal transduction.
R-HSA-167590. Nef Mediated CD4 Down-regulation.
R-HSA-173107. Binding and entry of HIV virion.
R-HSA-175474. Assembly Of The HIV Virion.
R-HSA-182218. Nef Mediated CD8 Down-regulation.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein NefUniRule annotation
Alternative name(s):
3'ORFUniRule annotation
Negative factorUniRule annotation
Short name:
F-proteinUniRule annotation
Cleaved into the following chain:
C-terminal core proteinUniRule annotation
Gene namesi
Name:nefUniRule annotation
OrganismiHuman immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1)
Taxonomic identifieri11706 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000105453 Componenti: Genome
  • UP000002241 Componenti: Genome

Subcellular locationi

  • Host cell membrane UniRule annotation; Lipid-anchor UniRule annotation; Cytoplasmic side UniRule annotation
  • Virion UniRule annotation
  • Secreted UniRule annotation1 Publication
  • Host Golgi apparatus membrane UniRule annotation

  • 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.UniRule annotation1 Publication

GO - Cellular componenti

Keywords - Cellular componenti

Host cell membrane, Host Golgi apparatus, Host membrane, Membrane, Secreted, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi20M → A: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is internalized but not sequestred in TGN. 1 Publication1
Mutagenesisi62 – 65EEEE → AAAA: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is not internalized. Reduced interaction with host PACS1 and PACS2. 2 Publications4
Mutagenesisi62 – 65EEEE → AAEA: About 50% loss of Nef-induced MHC-I down-regulation. 2 Publications4
Mutagenesisi62 – 65EEEE → AEAA: About 50% loss of Nef-induced MHC-I down-regulation. 2 Publications4
Mutagenesisi62 – 65EEEE → DDDD: No effect on Nef-induced MHC-I down-regulation. 2 Publications4
Mutagenesisi62 – 64EEE → AAA: About 50% loss of Nef-induced MHC-I down-regulation. 3
Mutagenesisi62 – 63EE → AA: Almost no effect on Nef-induced MHC-I down-regulation. 2
Mutagenesisi63 – 65EEE → AAA: About 50% loss of Nef-induced MHC-I down-regulation. 1 Publication3
Mutagenesisi63 – 64EE → AA: Almost no effect on Nef-induced MHC-I down-regulation. 2
Mutagenesisi64 – 65EE → AA: Almost no effect on Nef-induced MHC-I down-regulation. 2
Mutagenesisi72P → A: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is not internalized; when associated with A-75. 1 Publication1
Mutagenesisi75P → A: Complete loss of Nef-induced MHC-I down-regulation, MHC-I is not internalized; when associated with A-72. 1 Publication1
Mutagenesisi123D → E: Complete loss of Nef-induced MHC-I down-regulation, CD4 down-regulation, and enhancement of infectivity. Activates PAK2 twofold over wild-type levels. 1

Keywords - Diseasei

AIDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostUniRule annotation
ChainiPRO_00000383652 – 206Protein NefUniRule annotationAdd BLAST205
ChainiPRO_000003836658 – 206C-terminal core proteinUniRule annotationAdd BLAST149

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by hostUniRule annotation1
Modified residuei6Phosphoserine; by hostUniRule annotation1

Post-translational modificationi

Phosphorylated on serine residues, probably by host PKCdelta and theta.UniRule annotation
Myristoylated.UniRule annotation
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.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei57 – 58Cleavage; by viral proteaseUniRule annotation2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Expressioni

Inductioni

Expressed early in the viral replication cycle.UniRule annotation1 Publication

Keywords - Developmental stagei

Early protein

Interactioni

Subunit structurei

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.UniRule annotation7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ACOT8O147347EBI-6164028,EBI-1237371From Homo sapiens.

GO - Molecular functioni

Protein-protein interaction databases

BioGridi1205545. 70 interactors.
DIPiDIP-61724N.
IntActiP04601. 8 interactors.

Structurei

Secondary structure

1206
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi81 – 94Combined sources14
Helixi104 – 118Combined sources15
Beta strandi130 – 132Combined sources3
Beta strandi136 – 138Combined sources3
Beta strandi143 – 147Combined sources5
Helixi150 – 157Combined sources8
Helixi167 – 170Combined sources4
Beta strandi172 – 175Combined sources4
Beta strandi181 – 185Combined sources5
Helixi188 – 191Combined sources4
Helixi194 – 198Combined sources5
Helixi200 – 202Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RL2X-ray2.39C73-82[»]
4NEEX-ray2.88C/E/H/K63-203[»]
4WU5X-ray2.40C/F134-141[»]
4WU7X-ray2.30C/F136-141[»]
5HGAX-ray2.20C/F136-141[»]
5HGBX-ray2.40C/F/I/L134-141[»]
5HGDX-ray2.07C/F136-142[»]
5HGHX-ray2.39C134-142[»]
SMRiP04601.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni62 – 65Acidic; interacts with host PACS1 and PACS2; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalizationUniRule annotation2 Publications4
Regioni69 – 78SH3-binding; interaction with Src family tyrosine kinasesUniRule annotation10
Regioni108 – 124Mediates dimerization, Nef-PTE1 interactionUniRule annotationAdd BLAST17
Regioni148 – 180Binding to ATP6V1HUniRule annotationAdd BLAST33

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi72 – 75PxxP; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalizationUniRule annotation1 Publication4
Motifi164 – 165Dileucine internalization motif; necessary for CD4 internalizationUniRule annotation1 Publication2
Motifi174 – 175Diacidic; necessary for CD4 internalizationUniRule annotation2

Domaini

The dileucine internalization motif and a diacidic motif seem to be required for binding to AP-2.UniRule annotation
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.UniRule annotation1 Publication
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.UniRule annotation
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.UniRule annotation

Sequence similaritiesi

Belongs to the lentivirus primate group Nef protein family.UniRule annotation

Keywords - Domaini

SH3-binding

Phylogenomic databases

OrthoDBiVOG090000RB.

Family and domain databases

Gene3Di3.30.62.10. 1 hit.
4.10.890.10. 1 hit.
HAMAPiMF_04078. NEF_HIV. 1 hit.
InterProiView protein in InterPro
IPR027480. HIV-1_Nef_anchor.
IPR027481. HIV-1_Nef_core.
IPR001558. HIV_Nef.
PfamiView protein in Pfam
PF00469. F-protein. 1 hit.
SUPFAMiSSF55671. SSF55671. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04601-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGGKWSKSSV IGWPTVRERM RRAEPAADRV GAASRDLEKH GAITSSNTAA
60 70 80 90 100
TNAACAWLEA QEEEEVGFPV TPQVPLRPMT YKAAVDLSHF LKEKGGLEGL
110 120 130 140 150
IHSQRRQDIL DLWIYHTQGY FPDWQNYTPG PGVRYPLTFG WCYKLVPVEP
160 170 180 190 200
DKIEEANKGE NTSLLHPVSL HGMDDPEREV LEWRFDSRLA FHHVARELHP

EYFKNC
Length:206
Mass (Da):23,469
Last modified:February 9, 2010 - v5
Checksum:i5A26976E95483E9C
GO

Sequence cautioni

The sequence AAB50263 differs from that shown. Readthrough of a premature stop codon in position 123 that truncates the Nef protein. The sequence displayed is that of wild-type full-length HXB2-R7 clone.Curated
The sequence AAC82597 differs from that shown. Readthrough of a premature stop codon in position 123 that truncates the Nef protein. The sequence displayed is that of wild-type full-length HXB2-R7 clone.Curated
The sequence CAA26946 differs from that shown. Readthrough of a premature stop codon in position 123 that truncates the Nef protein. The sequence displayed is that of wild-type full-length HXB2-R7 clone.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti29R → G in CAA26946 (PubMed:2999715).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03187 Genomic RNA. Translation: CAA26946.1. Sequence problems.
K03455 Genomic RNA. Translation: AAB50263.1. Sequence problems.
AF033819 Genomic RNA. Translation: AAC82597.1. Sequence problems.
RefSeqiNP_057857.2. NC_001802.1.

Genome annotation databases

GeneIDi156110.
KEGGivg:156110.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiNEF_HV1H2
AccessioniPrimary (citable) accession number: P04601
Secondary accession number(s): O09780, Q85587
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: February 9, 2010
Last modified: July 5, 2017
This is version 141 of the entry and version 5 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families