Primary Citation PubMed: 9194185
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PrDOS: prediction of disordered protein regions from amino acid sequence.
(2007) Nucleic Acids Res 35
PubMed: 17567614 | PubMedCentral: PMC1933209 | DOI: 10.1093/nar/gkm363
An example of the prediction result page for HIV-1 NEF (PDB code: 2NEF).
Publication Year: 2007
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
(2008) PLoS Comput Biol 4
PubMed: 18989394 | PubMedCentral: PMC2566816 | DOI: 10.1371/journal.pcbi.1000214
Thus, the following structures were used: Gag derived proteins: matrix p17, capsid p24, nucleocapsid p7 (PDB IDs: 1tam, 1e6j, 1a1t, respectively); Pol derived proteins: protease p10, reverse transcrip... ase p51, RNase p15, integrase p31 (PDB IDs: 1aaq, 1rtd, 1o1w, 2itg, respectively); Vpr p12/p10 (PDB ID: 1m8l); Tat p16/p14 (PDB ID: 1mnb); Rev p19 (PDB ID: 1etf); Vpu p16 (PDB ID: 1vpu); Env derived proteins: gp120, gp41 (PDB IDs: 1gc1, 1env, respectively); Nef p27/p25 (PDB ID: 2nef).
Publication Year: 2008
An MHC-I cytoplasmic domain/HIV-1 Nef fusion protein binds directly to the mu subunit of the AP-1 endosomal coat complex.
(2009) PLoS One 4
PubMed: 20020046 | PubMedCentral: PMC2791223 | DOI: 10.1371/journal.pone.0008364
For reference, NMR structures of Nef residues 2–57 (PDB code: 1QA5)  and residues 56–206 (PDB code: 2NEF)  are used.
Publication Year: 2009
Small molecule inhibition of HIV-1-induced MHC-I down-regulation identifies a temporally regulated switch in Nef action.
(2010) Mol Biol Cell 21
PubMed: 20702582 | PubMedCentral: PMC2947465 | DOI: 10.1091/mbc.E10-05-0470
(F) Structural mapping of the chemical shift changes in the 1 H- 15 N HSQC spectrum of Nef induced by 2c onto the Nef NMR structure (PDB ID: 2NEF , see ( Grzesiek et al. , 1997 )).
More pronounced chemical shift changes (>0.1ppm) were observed for the resonances of Y 135 , K 144 , V 146 , K 184 (R 184 in Figure 1 F [PDB ID: 2NEF ]), F 185 , and L 189 which are clustered on the opposite side of the SH3 domain binding site.
Publication Year: 2010
HIV-1 nef protein structures associated with brain infection and dementia pathogenesis.
(2011) PLoS One 6
PubMed: 21347424 | PubMedCentral: PMC3036659 | DOI: 10.1371/journal.pone.0016659
Generation of nef 3D structures A structural model of the complete nef protein was assembled from partial structures published in the Research Collaboratory for Structural Bioinformatics (RCSB) Protei... Data Bank (PDB) as follows: a core domain structure spanning residues 56–159 and 175–206 (numbering relative to the HIV reference sequence HXB2; RCSB PDB accession number 2NEF]); and an anchor domain structure spanning residues 2–57 (RCSB PDB accession number 1QA5).
HIV-1 nef structural analysis Figure 2A shows the structure of the complete nef protein obtained by combining PDB structures 2NEF (transmembrane domain) and 1QA5 (myristoylation domain).
Publication Year: 2011
Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef.
PubMed: 21738584 | PubMedCentral: PMC3125164 | DOI: 10.1371/journal.pone.0020735
a ) Sequence logos of four hotspots on Nef separated by subtypes; b) Regions covered by hotspots highlighted in red on 3D structure of Nef visualized from the PDB structure 2NEF  .
HIV protein sequence hotspots for crosstalk with host hub proteins.
PubMed: 21858059 | PubMedCentral: PMC3156123 | DOI: 10.1371/journal.pone.0023293
PDB structures 1TBC  , 2X7L  , and 2NEF  were used respectively.
The identification of a small molecule compound that reduces HIV-1 Nef-mediated viral infectivity enhancement.
PubMed: 22110726 | PubMedCentral: PMC3217016 | DOI: 10.1371/journal.pone.0027696
First, homology modeling  –  was used to construct the model structure of HIV-1 Nef SF2 strain using its NMR structure (PDB code: 2NEF)  as a template.
Overlapping effector interfaces define the multiple functions of the HIV-1 Nef polyproline helix.
(2012) Retrovirology 9
PubMed: 22651890 | PubMedCentral: PMC3464899 | DOI: 10.1186/1742-4690-9-47
The modified BH10 Nef (PDB: 2NEF) presented has a truncated N-terminal arm (amino acids 1–55) and has a deletion of the flexible internal loop (amino acids 159–173).
Publication Year: 2012
In-silico designing of a potent analogue against HIV-1 Nef protein and protease by predicting its interaction network with host cell proteins.
(2013) J Pharm Bioallied Sci 5
PubMed: 23559827 | PubMedCentral: PMC3612342 | DOI: 10.4103/0975-7406.106572
Figure 5 (a) Docked structure of LOPI1 and 2NEF, visualized in PyMOL (Yellow dotted line show hydrogen bonds) (b) Docked structure of LOPI1and 2NEF, visualized in PMV (c) Docked structure of Lopinavir... and 1HPV, visualized in PyMOL (d) Docked structure of Lopinavir and 1HPV, visualized in PMV (e) Docked structure of LOPI1 and 1HPV, visualized in PyMOL (f) Docked structure of LOPI1 and 1HPV, visualized in PMV Table 4 Docking studies of lopinavir and LOPI1 with HIV Protease (1HPV) and HIV-1 Nef (2NEF) Discussion The brutal attack on humanity by HIV-1 has been already proven to be afflictingly difficult to hinder.
Publication Year: 2013
HIV's Nef interacts with ?-catenin of the Wnt signaling pathway in HEK293 cells.
(2013) PLoS One 8
PubMed: 24130899 | PubMedCentral: PMC3795062 | DOI: 10.1371/journal.pone.0077865
In addition, the HIV-1 Nef NMR structures (pdb code: 2nef, [ 39 ]) reveal that the putative β-catenin binding fragment is accessible on the surface of the protein, albeit in a different confor... ation from that adopted by the equivalent segment in E-cadherin bound to β-catenin ( Figure 2A ).
A. Superimposition of all 40 NMR structures of Nef (pdb code 2nef).
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