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110  structures 27  species 7  interactions 27  sequences 1  architecture

Family: F-protein (PF00469)

Summary: Negative factor, (F-Protein) or Nef

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Nef (protein) Edit Wikipedia article

Negative factor, (F-Protein) or Nef
NMR structure of the NEF protein based on the PDB: 2NEF​ coordinates.
OPM superfamily269
OPM protein2nef

Nef (Negative Regulatory Factor) is a small 27-35 kDa myristoylated protein encoded by primate lentiviruses. These include Human Immunodeficiency Viruses (HIV-1 and HIV-2) and Simian Immunodeficiency Virus (SIV). Nef localizes primarily to the cytoplasm but also partially to the Plasma Membrane (PM) and is one of many pathogen-expressed proteins, known as virulence factors, which function to manipulate the host's cellular machinery and thus allow infection, survival or replication of the pathogen.[1] Nef stands for "Negative Factor" and although it is often considered dispensable for HIV-1 replication, in infected hosts the viral protein markedly elevates viral titers.[2]


The expression of Nef early in the viral life cycle ensures T-cell activation and the establishment of a persistent state of infection, two basic attributes of HIV infection. Viral expression of Nef induces numerous changes within the infected cell including the modulation of protein cell surface expression, cytoskeletal remodeling, and signal transduction. Since the activation state of the infected cell plays an important role in the success rate of HIV-1 infection, it is important that resting T-cells be primed to respond to T-cell receptor (TCR) stimuli. HIV-1 Nef lowers the threshold for activation of CD4+ lymphocytes, but is not sufficient to cause activation in the absence of exogenous stimuli.[3]

By down regulating cell surface expression of CD4 and Lck, Nef creates a narrow TCR response which likely optimizes HIV-1 viral production and generates a susceptible population of cells to further infect. Nef retargets kinase-active Lck away from the plasma membrane to early and recycling endosomes (RE) as well as the Trans-Golgi network (TGN). RE/TGN associated Lck sub-populations in Nef expressing cells are in the catalytically active conformation and thus signaling competent.[4] While TCR signaling takes place at the plasma membrane (PM), activation of the Ras-GTPase takes place in intracellular compartments including the Golgi apparatus. Nef induced enrichment of active Lck in these compartments results in an increase of localized RAS activity and enhanced activation of Erk kinase and the production of Interleukin-2 (IL-2).[5] Since IL-2 is known to activate the growth, proliferation, and differentiation of T-cells to become effector T-cells; this is a self-serving effect that creates a new population of cells which HIV-1 is able to infect. Self-activation of the infected cell by IL-2 also stimulates the cell to become an effector cell and initiate the machinery which HIV-1 relies upon for its own proliferation.

To further evade the host immune response, Nef down-regulates the cell surface and total expression of the negative immune modulator CTLA-4 by targeting the protein for lysosomal degradation. In contrast to CD28 which activates T-cells, CTLA-4 is essentially an “off-switch” which would inhibit the viral production if it were activated. Lentiviruses such as HIV-1 have acquired proteins such as Nef which perform a wide array of functions including the identification of CTLA-4 before it reaches the PM and tagging it for degradation.[6] Nef is also known to phosphorylate and inactivate Bad, a proapoptotic member of the Bcl-2 family thus protecting the infected cells from apoptosis.[citation needed]

Cytoskeletal remodeling is thought to reduce TCR signaling during early infection and is also modulated to some degree by Nef. Actin remodeling is generally modulated by the actin severing factor cofilin. Nef is able to associate with the cellular kinase PAK2 which phosphorylates and inactivates cofilin and interferes with early TCR signaling.

Clinical significance

The Sydney blood bank cohort (SBBC) were a group of eight patients who were asymptomatic many years after initial infection by transfusion from an infected blood donor. Later analyses showed that the virus strain was a Nef-deleted variant.[7]


A Nef-deleted virus vaccine has not been tried in humans although it was successfully tested in Rhesus macaques.[8][9]

See also


  1. ^ Das SR, Jameel S (April 2005). "Biology of the HIV Nef protein" (PDF). Indian J. Med. Res. 121 (4): 315–32. PMID 15817946.
  2. ^ Marcey D, Somple M, Silva N (2007-01-01). "HIV-1 Nef Protein". The Online Macromolecular Museum Exhibits. California Lutheran University. Retrieved 2008-08-06.
  3. ^ Abraham L, Fackler OT (December 2012). "HIV-1 Nef: a multifaceted modulator of T cell receptor signaling". Cell Communication and Signaling. 10 (1): 39. doi:10.1186/1478-811X-10-39. PMC 3534016. PMID 23227982.
  4. ^ Laguette N, Bregnard C, Benichou S, Basmaciogullari S (June 2010). "Human immunodeficiency virus (HIV) type-1, HIV-2 and simian immunodeficiency virus Nef proteins". Mol. Aspects Med. 31 (5): 418–33. doi:10.1016/j.mam.2010.05.003. PMID 20594957.
  5. ^ Geyer M, Fackler OT, Peterlin BM (July 2001). "Structure–function relationships in HIV-1 Nef". EMBO Reports. 2 (7): 580–5. doi:10.1093/embo-reports/kve141. PMC 1083955. PMID 11463741.
  6. ^ El-Far M, Isabelle C, Chomont N, Bourbonnière M, Fonseca S, Ancuta P, Peretz Y, Chouikh Y, Halwani R, Schwartz O, Madrenas J, Freeman GJ, Routy JP, Haddad EK, Sékaly RP (January 2013). "Down-Regulation of CTLA-4 by HIV-1 Nef Protein". PLoS ONE. 8 (1): e54295. Bibcode:2013PLoSO...854295E. doi:10.1371/journal.pone.0054295. PMC 3553160. PMID 23372701.
  7. ^ Learmont JC, Geczy AF, Mills J, Ashton LJ, Raynes-Greenow CH, Garsia RJ, Dyer WB, McIntyre L, Oelrichs RB, Rhodes DI, Deacon NJ, Sullivan JS (June 1999). "Immunologic and virologic status after 14 to 18 years of infection with an attenuated strain of HIV-1. A report from the Sydney Blood Bank Cohort". N. Engl. J. Med. 340 (22): 1715–22. doi:10.1056/NEJM199906033402203. PMID 10352163.
  8. ^ Daniel MD, Kirchhoff F, Czajak SC, Sehgal PK, Desrosiers RC (December 1992). "Protective effects of a live attenuated SIV vaccine with a deletion in the nef gene". Science. 258 (5090): 1938–41. Bibcode:1992Sci...258.1938D. doi:10.1126/science.1470917. PMID 1470917.
  9. ^ Muthumani K, Choo AY, Hwang DS, Premkumar A, Dayes NS, Harris C, Green DR, Wadsworth SA, Siekierka JJ, Weiner DB (September 2005). "HIV-1 Nef-induced FasL induction and bystander killing requires p38 MAPK activation". Blood. 106 (6): 2059–68. doi:10.1182/blood-2005-03-0932. PMC 1895138. PMID 15928037.

Further reading

External links

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Negative factor, (F-Protein) or Nef Provide feedback

Nef protein accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src kinase family.

Literature references

  1. Arold S, Franken P, Strub M-P, Hoh F, Benichou S, Benarous R, Dumas C; , Structure 1997;5:1361-1372.: The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signalling PUBMED:9351809 EPMC:9351809

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001558

Human immunodeficiency virus 1 (HIV-1) negative factor (Nef protein) accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases [PUBMED:9351809].

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Seed source: Pfam-B_128 (release 1.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 20
Number in full: 27
Average length of the domain: 209.80 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 95.77 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 15.0
Trusted cut-off 27.0 46.3
Noise cut-off 19.3 14.9
Model length: 220
Family (HMM) version: 21
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ITAM SH3_1 Adap_comp_sub Adap_comp_sub MHC_I SH3_1 F-protein


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the F-protein domain has been found. There are 110 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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