PDBsum entry 2nef

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Regulatory factor PDB id
Protein chain
136 a.a. *
* Residue conservation analysis
PDB id:
Name: Regulatory factor
Title: HIV-1 nef (regulatory factor), nmr, 40 structures
Structure: Negative factor (f-protein). Chain: a. Synonym: HIV-1 nef. Engineered: yes. Mutation: yes
Source: Human immunodeficiency virus type 1. Organism_taxid: 11678. Strain: bh10. Gene: HIV-1 nef. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 40 models
Authors: S.Grzesiek,A.Bax,G.M.Clore,A.M.Gronenborn,J.S.Hu,J.Kaufman,I S.J.Stahl,N.Tjandra,P.T.Wingfield
Key ref:
S.Grzesiek et al. (1997). Refined solution structure and backbone dynamics of HIV-1 Nef. Protein Sci, 6, 1248-1263. PubMed id: 9194185 DOI: 10.1002/pro.5560060613
12-Feb-97     Release date:   07-Jul-97    
Supersedes: 1nef
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q70627  (NEF_HV1LW) -  Protein Nef
206 a.a.
136 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     GTP binding     1 term  


DOI no: 10.1002/pro.5560060613 Protein Sci 6:1248-1263 (1997)
PubMed id: 9194185  
Refined solution structure and backbone dynamics of HIV-1 Nef.
S.Grzesiek, A.Bax, J.S.Hu, J.Kaufman, I.Palmer, S.J.Stahl, N.Tjandra, P.T.Wingfield.
The tendency of HIV-1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three-dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340-345) and for X-ray crystallography (Lee et al., 1996, Cell 85:931-942). Methods used to determine the Nef structure by NMR at pH 8 and 0.6 mM concentration are presented, together with a detailed description of Nef's secondary and tertiary structure. The described techniques have general applicability for the NMR structure determination of proteins that are aggregating and/or have limited stability at low pH values. Extensive chemical shift assignments are reported for backbone and side chain 1H, 13C, and 15N resonances of the HIV-1 Nef deletion mutants NEF delta 2-39, NEF delta 2-39, delta 159-173, and of NEF delta 2-39, delta 159-173 in complex with the SH3 domain of the Hck tyrosine protein kinase. Besides a type II polyproline helix, Nef's structure consists of three alpha-helices, a 3(10) helix, and a five-stranded anti-parallel beta-sheet. The analysis of 15N relaxation parameters of the backbone amide sites reveals that all the secondary structure elements are non-mobile on the picosecond to nanosecond and on the millisecond time scale. A large number of slowly exchanging amide protons provides evidence for the stability of the Nef core even on the time scale of hours. Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops. The residues of the HIV-1 protease cleavage site (W57/L58) do not exhibit large amplitude motions on the sub-nanosecond time scale, and their side chains insert themselves into a hydrophobic crevice formed between the C-terminus of helix 1 and the N-terminus of helix 2. A refined structure has been determined based on additional constraints for side-chain and backbone dihedral angles derived from a large number of three-bond J-coupling and ROE data.
  Selected figure(s)  
Figure 3.
Fig. 3. 'H-I5N HSC pectrum of NEF'2-39 together with assignments for the most well-resolved residues.Resonancesmarked by asterisksarealiased in the 15N dimension.Dashedlinesmark NH2 groups of Asn and Gln residues.
Figure 11.
Fig. 11. N TI, Tz and heteronuclear { 'H)-N NOE relaxation data for NEFA2-39.159-173 as of residue number.
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1997, 6, 1248-1263) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22705789 X.Jia, R.Singh, S.Homann, H.Yang, J.Guatelli, and Y.Xiong (2012).
Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef.
  Nat Struct Mol Biol, 19, 701-706.
PDB codes: 4emz 4en2
  21365684 J.Jung, I.J.Byeon, J.Ahn, and A.M.Gronenborn (2011).
Structure, dynamics, and Hck interaction of full-length HIV-1 Nef.
  Proteins, 79, 1609-1622.  
21336563 J.L.Foster, S.J.Denial, B.R.Temple, and J.V.Garcia (2011).
Mechanisms of HIV-1 Nef Function and Intracellular Signaling.
  J Neuroimmune Pharmacol, 6, 230-246.  
21213249 N.C.Fitzkee, D.A.Torchia, and A.Bax (2011).
Measuring rapid hydrogen exchange in the homodimeric 36 kDa HIV-1 integrase catalytic core domain.
  Protein Sci, 20, 500-512.  
20927614 S.A.Dames, A.Schönichen, and M.Geyer (2011).
(1)H, (15)N, and (13)C assignments of the N-terminal activation domain of Dictyostelium discoideum Formin C.
  Biomol NMR Assign, 5, 47-49.  
21259120 S.Mäntylahti, M.Hellman, and P.Permi (2011).
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins.
  J Biomol NMR, 49, 99.  
19782103 C.S.Adamson, and E.O.Freed (2010).
Novel approaches to inhibiting HIV-1 replication.
  Antiviral Res, 85, 119-141.  
20702582 J.D.Dikeakos, K.M.Atkins, L.Thomas, L.Emert-Sedlak, I.J.Byeon, J.Jung, J.Ahn, M.D.Wortman, B.Kukull, M.Saito, H.Koizumi, D.M.Williamson, M.Hiyoshi, E.Barklis, M.Takiguchi, S.Suzu, A.M.Gronenborn, T.E.Smithgall, and G.Thomas (2010).
Small molecule inhibition of HIV-1-induced MHC-I down-regulation identifies a temporally regulated switch in Nef action.
  Mol Biol Cell, 21, 3279-3292.  
20504918 L.Dai, and M.Stevenson (2010).
A novel motif in HIV-1 Nef that regulates MIP-1beta chemokine release in macrophages.
  J Virol, 84, 8327-8331.  
20042596 S.A.Dames (2010).
Structural basis for the association of the redox-sensitive target of rapamycin FATC domain with membrane-mimetic micelles.
  J Biol Chem, 285, 7766-7775.
PDB codes: 2kio 2kit
20124696 W.M.Kim, A.B.Sigalov, and L.J.Stern (2010).
Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
  Acta Crystallogr D Biol Crystallogr, 66, 163-175.
PDB codes: 3ik5 3ioz
  20659345 Y.J.Jin, X.Zhang, C.Y.Cai, and S.J.Burakoff (2010).
Alkylating HIV-1 Nef - a potential way of HIV intervention.
  AIDS Res Ther, 7, 26.  
  20863404 Y.T.Kwak, A.Raney, L.S.Kuo, S.J.Denial, B.R.Temple, J.V.Garcia, and J.L.Foster (2010).
Self-association of the Lentivirus protein, Nef.
  Retrovirology, 7, 77.  
20020046 R.K.Singh, D.Lau, C.M.Noviello, P.Ghosh, and J.C.Guatelli (2009).
An MHC-I cytoplasmic domain/HIV-1 Nef fusion protein binds directly to the micro subunit of the AP-1 endosomal coat complex.
  PLoS One, 4, e8364.  
19279667 T.L.Lau, C.Kim, M.H.Ginsberg, and T.S.Ulmer (2009).
The structure of the integrin alphaIIbbeta3 transmembrane complex explains integrin transmembrane signalling.
  EMBO J, 28, 1351-1361.
PDB code: 2k9j
19297321 X.Hanoulle, A.Badillo, J.M.Wieruszeski, D.Verdegem, I.Landrieu, R.Bartenschlager, F.Penin, and G.Lippens (2009).
Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B.
  J Biol Chem, 284, 13589-13601.  
  18808677 J.L.Foster, and J.V.Garcia (2008).
HIV-1 Nef: at the crossroads.
  Retrovirology, 5, 84.  
18653452 L.L.Baugh, J.V.Garcia, and J.L.Foster (2008).
Functional characterization of the human immunodeficiency virus type 1 Nef acidic domain.
  J Virol, 82, 9657-9667.  
18032517 O.W.Lindwasser, W.J.Smith, R.Chaudhuri, P.Yang, J.H.Hurley, and J.S.Bonifacino (2008).
A diacidic motif in human immunodeficiency virus type 1 Nef is a novel determinant of binding to AP-2.
  J Virol, 82, 1166-1174.  
17140399 A.Burtey, J.Z.Rappoport, J.Bouchet, S.Basmaciogullari, J.Guatelli, S.M.Simon, S.Benichou, and A.Benmerah (2007).
Dynamic interaction of HIV-1 Nef with the clathrin-mediated endocytic pathway at the plasma membrane.
  Traffic, 8, 61-76.  
  17908312 B.Brügger, E.Krautkrämer, N.Tibroni, C.E.Munte, S.Rauch, I.Leibrecht, B.Glass, S.Breuer, M.Geyer, H.G.Kräusslich, H.R.Kalbitzer, F.T.Wieland, and O.T.Fackler (2007).
Human immunodeficiency virus type 1 Nef protein modulates the lipid composition of virions and host cell membrane microdomains.
  Retrovirology, 4, 70.  
17360486 M.Christen, B.Christen, M.G.Allan, M.Folcher, P.Jenö, S.Grzesiek, and U.Jenal (2007).
DgrA is a member of a new family of cyclic diguanosine monophosphate receptors and controls flagellar motor function in Caulobacter crescentus.
  Proc Natl Acad Sci U S A, 104, 4112-4117.  
17724342 S.A.Dames, A.Schönichen, A.Schulte, M.Barboric, B.M.Peterlin, S.Grzesiek, and M.Geyer (2007).
Structure of the Cyclin T binding domain of Hexim1 and molecular basis for its recognition of P-TEFb.
  Proc Natl Acad Sci U S A, 104, 14312-14317.
PDB code: 2gd7
16415008 E.O'Neill, L.S.Kuo, J.F.Krisko, D.R.Tomchick, J.V.Garcia, and J.L.Foster (2006).
Dynamic evolution of the human immunodeficiency virus type 1 pathogenic factor, Nef.
  J Virol, 80, 1311-1320.  
16501114 K.Agopian, B.L.Wei, J.V.Garcia, and D.Gabuzda (2006).
A hydrophobic binding surface on the human immunodeficiency virus type 1 Nef core is critical for association with p21-activated kinase 2.
  J Virol, 80, 3050-3061.  
17209762 M.Kumar, S.K.Jain, S.T.Pasha, D.Chattopadhaya, S.Lal, and A.Rai (2006).
Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV type 1: emergence of a distinct subclade and predicted implications.
  AIDS Res Hum Retroviruses, 22, 1206-1219.  
17075134 O.K.Baryshnikova, and B.D.Sykes (2006).
Backbone dynamics of SDF-1alpha determined by NMR: interpretation in the presence of monomer-dimer equilibrium.
  Protein Sci, 15, 2568-2578.  
15632291 M.Matsubara, T.Jing, K.Kawamura, N.Shimojo, K.Titani, K.Hashimoto, and N.Hayashi (2005).
Myristoyl moiety of HIV Nef is involved in regulation of the interaction with calmodulin in vivo.
  Protein Sci, 14, 494-503.  
14695515 G.Lippens, J.M.Wieruszeski, A.Leroy, C.Smet, A.Sillen, L.Buée, and I.Landrieu (2004).
Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites.
  Chembiochem, 5, 73-78.  
15329414 I.Landrieu, M.da Costa, L.De Veylder, F.Dewitte, K.Vandepoele, S.Hassan, J.M.Wieruszeski, F.Corellou, J.D.Faure, M.Van Montagu, D.Inzé, and G.Lippens (2004).
A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana.
  Proc Natl Acad Sci U S A, 101, 13380-13385.
PDB code: 1t3k
12682015 J.D.Kahmann, H.J.Sass, M.G.Allan, H.Seto, C.J.Thompson, and S.Grzesiek (2003).
Structural basis for antibiotic recognition by the TipA class of multidrug-resistance transcriptional regulators.
  EMBO J, 22, 1824-1834.
PDB code: 1ny9
14691137 K.Janvier, Y.Kato, M.Boehm, J.R.Rose, J.A.Martina, B.Y.Kim, S.Venkatesan, and J.S.Bonifacino (2003).
Recognition of dileucine-based sorting signals from HIV-1 Nef and LIMP-II by the AP-1 gamma-sigma1 and AP-3 delta-sigma3 hemicomplexes.
  J Cell Biol, 163, 1281-1290.  
12502873 T.Yamada, N.Kaji, T.Odawara, J.Chiba, A.Iwamoto, and Y.Kitamura (2003).
Proline 78 is crucial for human immunodeficiency virus type 1 Nef to down-regulate class I human leukocyte antigen.
  J Virol, 77, 1589-1594.  
12237454 S.Bhattacharya, M.V.Botuyan, F.Hsu, X.Shan, A.I.Arunkumar, C.H.Arrowsmith, A.M.Edwards, and W.J.Chazin (2002).
Characterization of binding-induced changes in dynamics suggests a model for sequence-nonspecific binding of ssDNA by replication protein A.
  Protein Sci, 11, 2316-2325.  
  11463741 M.Geyer, O.T.Fackler, and B.M.Peterlin (2001).
Structure--function relationships in HIV-1 Nef.
  EMBO Rep, 2, 580-585.  
15992165 S.H.Coleman, J.R.Day, and J.C.Guatelli (2001).
The HIV-1 Nef protein as a target for antiretroviral therapy.
  Expert Opin Ther Targets, 5, 1.  
  11152126 B.E.Ramirez, O.N.Voloshin, R.D.Camerini-Otero, and A.Bax (2000).
Solution structure of DinI provides insight into its mode of RecA inactivation.
  Protein Sci, 9, 2161-2169.
PDB codes: 1f0a 1ghh
11208125 D.E.Wakeham, J.A.Ybe, F.M.Brodsky, and P.K.Hwang (2000).
Molecular structures of proteins involved in vesicle coat formation.
  Traffic, 1, 393-398.  
10799608 L.X.Liu, N.Heveker, O.T.Fackler, S.Arold, S.Le Gall, K.Janvier, B.M.Peterlin, C.Dumas, O.Schwartz, S.Benichou, and R.Benarous (2000).
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.  
11106734 M.Suzuki, R.J.Youle, and N.Tjandra (2000).
Structure of Bax: coregulation of dimer formation and intracellular localization.
  Cell, 103, 645-654.
PDB code: 1f16
  10892807 S.Arold, F.Hoh, S.Domergue, C.Birck, M.A.Delsuc, M.Jullien, and C.Dumas (2000).
Characterization and molecular basis of the oligomeric structure of HIV-1 nef protein.
  Protein Sci, 9, 1137-1148.  
  9971776 A.Mangasarian, V.Piguet, J.K.Wang, Y.L.Chen, and D.Trono (1999).
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, 73, 1964-1973.  
10320324 J.J.Prompers, B.van Noorloos, M.L.Mannesse, A.Groenewegen, M.R.Egmond, H.M.Verheij, C.W.Hilbers, and H.A.Pepermans (1999).
NMR studies of Fusarium solani pisi cutinase in complex with phosphonate inhibitors.
  Biochemistry, 38, 5982-5994.  
10386338 V.Piguet, and D.Trono (1999).
The Nef protein of primate lentiviruses.
  Rev Med Virol, 9, 111-120.  
9759480 A.D.Frankel, and J.A.Young (1998).
HIV-1: fifteen proteins and an RNA.
  Annu Rev Biochem, 67, 1.  
9818269 R.A.Laskowski, M.W.MacArthur, and J.M.Thornton (1998).
Validation of protein models derived from experiment.
  Curr Opin Struct Biol, 8, 631-639.  
9778343 S.Arold, R.O'Brien, P.Franken, M.P.Strub, F.Hoh, C.Dumas, and J.E.Ladbury (1998).
RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef.
  Biochemistry, 37, 14683-14691.
PDB code: 1bu1
  9416624 P.Franken, S.Arold, A.Padilla, M.Bodeus, F.Hoh, M.P.Strub, M.Boyer, M.Jullien, R.Benarous, and C.Dumas (1997).
HIV-1 Nef protein: purification, crystallizations, and preliminary X-ray diffraction studies.
  Protein Sci, 6, 2681-2683.  
9351809 S.Arold, P.Franken, M.P.Strub, F.Hoh, S.Benichou, R.Benarous, and C.Dumas (1997).
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, 5, 1361-1372.
PDB codes: 1avv 1avz
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