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Q70627 (NEF_HV1LW) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protein Nef
Alternative name(s):
3'ORF
Negative factor
Short name=F-protein

Cleaved into the following chain:

  1. C-terminal core protein
Gene names
Name:nef
OrganismHuman immunodeficiency virus type 1 group M subtype B (isolate LW123) (HIV-1)
Taxonomic identifier82834 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length206 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

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. One of the earliest and most abundantly expressed viral proteins By similarity.

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) By similarity.

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 By similarity.

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. Interacts and decreases the half-life of p53, 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 By similarity.

Extracellular Nef protein targets CD4+ T-lymphocytes for apoptosis by interacting with CXCR4 surface receptors By similarity.

Subunit structure

Homodimer By similarity. 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 (via C-terminus). 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 TCR-zeta chain; this interaction up-regulates the Fas ligand (FasL) surface expression. Interacts with various cellular proteins including MAP3K5, beta-COP, HCK, and PTE1. Interacts with human GNB2L1/RACK1; this increases Nef phosphorylation by PKC By similarity.

Subcellular location

Host cell membrane; Lipid-anchor; Cytoplasmic side By similarity. Host cytoplasmhost perinuclear region By similarity. Virion By similarity. Secreted By similarity. Note: Predominantly found in the paranuclear area, probably in the TGN. Correct localization requires PACS1. Also associates with the inner plasma membrane through its N-terminal domain. Nef stimulates its own export via the release of exosomes. Also incorporated in virions at a rate of about 10 molecules per virion, where it is cleaved By similarity.

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 p53 By similarity.

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 By similarity.

The di-leucine internalization motif and a diacidic motif seem to be required for binding to AP-2 By similarity.

The acidic region may play a stabilizing role in the formation of a ternary complex between Nef, the MHC-I cytoplasmic domain, and AP1M1 By similarity.

Post-translational modification

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 By similarity.

Phosphorylated on serine residues, probably by host PKC By similarity.

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).

Sequence similarities

Belongs to the lentivirus primate group Nef protein family.

Ontologies

Keywords
   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
   Cellular componentHost cell membrane
Host cytoplasm
Host membrane
Membrane
Secreted
Virion
   Developmental stageEarly protein
   DiseaseAIDS
   DomainSH3-binding
   PTMLipoprotein
Myristate
Phosphoprotein
   Technical term3D-structure
Gene Ontology (GO)
   Biological_processapoptotic process

Inferred from electronic annotation. Source: UniProtKB-KW

negative regulation by symbiont of host T-cell mediated immune response

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of CD4 biosynthetic process

Inferred from sequence or structural similarity. Source: UniProtKB

pathogenesis

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of calcium-mediated signaling

Inferred from sequence or structural similarity. Source: UniProtKB

suppression by virus of host adaptive immune response

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I

Inferred from sequence or structural similarity. Source: UniProtKB

suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host autophagy

Inferred from electronic annotation. Source: UniProtKB-KW

viral life cycle

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componenthost cell perinuclear region of cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

membrane

Inferred from electronic annotation. Source: UniProtKB-KW

virion

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATPase binding

Inferred from sequence or structural similarity. Source: UniProtKB

CD4 receptor binding

Inferred from sequence or structural similarity. Source: UniProtKB

GTP binding

Inferred from electronic annotation. Source: InterPro

MHC class I protein binding

Inferred from sequence or structural similarity. Source: UniProtKB

SH3 domain binding

Inferred from sequence or structural similarity. Source: UniProtKB

calmodulin binding

Inferred from sequence or structural similarity. Source: UniProtKB

protein kinase binding

Inferred from sequence or structural similarity. Source: UniProtKB

receptor binding

Inferred from sequence or structural similarity. Source: UniProtKB

thioesterase binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 206205Protein Nef
PRO_0000038325
Chain58 – 206149C-terminal core protein By similarity
PRO_0000038326

Regions

Region2 – 5756N-terminal; associates with the host plasma membrane By similarity
Region7 – 2620Necessary for MHC-I internalization By similarity
Region62 – 654Acidic; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalization and interaction with host PACS1 and PACS2 By similarity
Region69 – 7810SH3-binding; interaction with Src family tyrosine kinases By similarity
Region108 – 12417Mediates dimerization, Nef-PTE1 interaction, Nef-induced CD4 and MHC-I down-regulation and enhancement of infectivity By similarity
Region148 – 18033Binding to ATP6V1H By similarity
Motif72 – 754PxxP; stabilizes the interaction of NEF/MHC-I with host AP1M1; necessary for MHC-I internalization By similarity
Motif164 – 1652Di-leucine internalization motif; necessary for CD4 internalization By similarity
Motif174 – 1752Diacidic; necessary for CD4 internalization By similarity

Sites

Site201Might play a role in AP-1 recruitment to the Nef-MHC-I complex By similarity
Site57 – 582Cleavage; by viral protease By similarity

Amino acid modifications

Lipidation21N-myristoyl glycine; by host By similarity

Secondary structure

...................... 206
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q70627 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: ED81F68F6B61278E

FASTA20623,414
        10         20         30         40         50         60 
MGGKWSKSSV IGWPTVRERM RRAEPAADGV GAASQDLEKH GAITSSNTAA TNADCAWLEA 

        70         80         90        100        110        120 
QEEEEVGFPV TPQVPLRPMT YKAAVDLSHF LKEKGGLEGL IHSQRRQDIL DLWIYHTQGY 

       130        140        150        160        170        180 
FPDWQNYTPG PGIRYPLTFG WCYKLVPVEP EKLEEANKGE NTSLLHPVSL HGMDDPEREV 

       190        200 
LEWRFDSRLA FHHVARELHP EYFKNC 

« Hide

References

[1]"Viral variability and serum antibody response in a laboratory worker infected with HIV type 1 (HTLV type IIIB)."
Reitz M.S. Jr., Hall L., Robert-Guroff M., Lautenberger J.A., Hahn B.M., Shaw G.M., Kong L.I., Weiss S.H., Waters D., Gallo R.C., Blattner W.
AIDS Res. Hum. Retroviruses 10:1143-1155(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"Refined solution structure and backbone dynamics of HIV-1 Nef."
Grzesiek S., Bax A., Hu J.S., Kaufman J., Palmer I., Stahl S.J., Tjandra N., Wingfield P.T.
Protein Sci. 6:1248-1263(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 56-206.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U12055 Genomic RNA. Translation: AAA76691.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2NEFNMR-A56-205[»]
ProteinModelPortalQ70627.
SMRQ70627. Positions 2-205.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.30.62.10. 1 hit.
4.10.890.10. 1 hit.
InterProIPR027480. HIV-1_Nef_anchor.
IPR027481. HIV-1_Nef_core.
IPR001558. HIV_Nef.
[Graphical view]
PfamPF00469. F-protein. 1 hit.
[Graphical view]
SUPFAMSSF55671. SSF55671. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ70627.

Entry information

Entry nameNEF_HV1LW
AccessionPrimary (citable) accession number: Q70627
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 100 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references