HIV-1 NEF Structures Index

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Tutorials and Museum Exhibits

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A tutorial on HIV-1 Nef structure/function was done by Maggie Somple, Nathan Silva, and David Marcey from the Online Macromolecular Museum at California Lutheran University.

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PDB Structure Entries

Links to NCBI Entrez PubMed for Publications on the structure.
Links to the Potein Structures Database (PDB) entry for the structure.
Links to a page that will open the Protein Explorer tool with the structure loaded. Protein Explorer can be downloaded and installed to run locally. More Information.
Opens the NCBI Structures Database entry for the structure. This NCBI site has the Cn3D structure viewing software, which required the NCBI ASN.1 structure format rather than the .PDB format. More information.

2NEF: Protein Sci 1997 Jun;6(6):1248-63.

HIV-1 Nef: 40 NMR structures.

1AVZ: Structure 1997 Oct 15;5(10):1361-72.

HIV-1 Nef protein in complex with wild type Fyn SH3 domain.

1AVV: Structure 1997 Oct 15;5(10):1361-72.

HIV-1 Nef core domain with segment missing.

1QA4: Structure 1997 Oct 15;5(10):1361-72.

HIV-1 Nef: 2 NMR models of N-terminal domain without myristoylation.

1QA5: Structure 1997 Oct 15;5(10):1361-72.

HIV-1 Nef: 2 NMR models of N-terminal domain with myristoylation.

1EFN: Cell 1996 Jun 14;85(6):931-42.

HIV-1 Nef Core domain complexed with Fyn protein (of the src family)SH3 domain.

1ZEC: Cell 1996 Jun 14;85(6):931-42.

HIV-1 nef, NMR structure of the N terminus (Nef 1-25).

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Publications on Nef Structures

Review
Arold ST, Baur AS.
Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein.
Trends Biochem Sci. 2001 Jun;26(6):356-63.
PMID: 11406408

Nef structure:
Geyer M, Peterlin BM.
Domain assembly, surface accessibility and sequence conservation in full length HIV-1 Nef.
FEBS Lett. 2001 May 11;496(2-3):91-5.
PMID: 11356189

Nef-MHC interaction:
Williams M, Roeth JF, Kasper MR, Fleis RI, Przybycin CG, Collins KL.
Direct binding of human immunodeficiency virus type 1 Nef to the major histocompatibility complex class I (MHC-I) cytoplasmic tail disrupts MHC-I trafficking.
J Virol. 2002 Dec;76(23):12173-84.
PMID: 12414957

Nef-CD4 interaction:
Mangasarian A, Piguet V, Wang JK, Chen YL, Trono D.
Nef-induced CD4 and major histocompatibility complex class I (MHC-I) down-regulation are governed by distinct determinants: N-terminal alpha helix and proline repeat of Nef selectively regulate MHC-I trafficking.
J Virol. 1999 Mar;73(3):1964-73.
PMID: 9971776

Nef-CD4 interaction:
Preusser A, Briese L, Willbold D. Related Articles, Links
Presence of a helix in human CD4 cytoplasmic domain promotes binding to HIV-1 Nef protein.
Biochem Biophys Res Commun. 2002 Apr 5;292(3):734-40.
PMID: 11922627

Nef:SH3 interaction:
Hiipakka M, Huotari P, Manninen A, Renkema GH, Saksela K.
Inhibition of cellular functions of HIV-1 Nef by artificial SH3 domains.
Virology. 2001 Jul 20;286(1):152-9.
PMID: 11448168

Nef:SH3 interaction:
Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C. Related Articles, Links
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 signaling.
Structure. 1997 Oct 15;5(10):1361-72.
PMID: 9351809

Nef:SH3 interaction:
Saksela K, Cheng G, Baltimore D.
Proline-rich (PxxP) motifs in HIV-1 Nef bind to SH3 domains of a subset of Src kinases and are required for the enhanced growth of Nef+ viruses but not for down-regulation of CD4.
EMBO J. 1995 Feb 1;14(3):484-91.
PMID: 7859737

Nef oligomerization:
Arold S, Hoh F, Domergue S, Birck C, Delsuc MA, Jullien M, Dumas C. Related Articles, Links
Characterization and molecular basis of the oligomeric structure of HIV-1 nef protein.
Protein Sci. 2000 Jun;9(6):1137-48.
PMID: 10892807

Myristoylation:
Geyer M, Munte CE, Schorr J, Kellner R, Kalbitzer HR. Related Articles, Links
Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein.
J Mol Biol. 1999 May 28;289(1):123-38.
PMID: 10339411

Nef Structure:
Franken P, Arold S, Padilla A, Bodeus M, Hoh F, Strub MP, Boyer M, Jullien M, Benarous R, Dumas C.
HIV-1 Nef protein: purification, crystallizations, and preliminary X-ray diffraction studies.
Protein Sci. 1997 Dec;6(12):2681-3.
PMID: 9416624

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