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Viral protein PDB id
1ce4
Jmol
Contents
Protein chain
35 a.a.
PDB id:
1ce4
Name: Viral protein
Title: Conformational model for the consensus v3 loop of the envelope protein gp120 of HIV-1
Structure: Protein (v3 loop of HIV-1 envelope protein). Chain: a. Engineered: yes. Other_details: this v3 loop peptide is a fragment of the gp120 envelope protein of HIV-1.
Source: Synthetic: yes. Other_details: sequence taken from human immunodeficiency virus type 1 (clone 12), gene env
NMR struc: 20 models
Authors: W.F.Vranken,F.Fant,M.Budesinsky,F.A.M.Borremans
Key ref:
W.F.Vranken et al. (1995). The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution. FEBS Lett, 374, 117-121. PubMed id: 7589496 DOI: 10.1016/0014-5793(95)01086-T
Date:
15-Mar-99     Release date:   18-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20871  (ENV_HV1JR) -  Envelope glycoprotein gp160
Seq:
Struc: 		 
Seq:
Struc: 		848 a.a.
35 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral envelope   1 term 

 

 
DOI no: 10.1016/0014-5793(95)01086-T FEBS Lett 374:117-121 (1995)
PubMed id: 7589496  
 
 
The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution.
W.F.Vranken, M.Budesinsky, F.Fant, K.Boulez, F.A.Borremans.
 
  ABSTRACT  
 
The disulfide bridge closed cyclic peptide corresponding to the whole Consensus V3 loop of the envelope protein gp120 of HIV-1 was examined by proton 2D-NMR spectroscopy in water and in a 20% trifluoroethanol/water solution. In water, NOE data support a beta-turn conformation for the central conservative GPGR region and point towards partial formation of a helix in the C-terminal part. Upon addition of trifluoroethanol, a C-terminal helix is formed. This is evidenced by NOE data, alpha-proton chemical shift changes and changes in the JN alpha vicinal coupling constants. The C-terminal helix is amphipathic and also occurs in other examined strains. It could therefore be an important feature for the functioning of the V3 loop.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Diagrams showig the sequential NOE connectivities and the NOE connectivities indicating secondary stucture observed in the water (A) and the 20% v/v TFE/water (B) solutions of the Consensus V3 loop peptide. 		Figure 2.
Fig. 2. iagrams showing the CT-NOE intensities of the NH resonance lines in F1 of th Consensus V3 loop peptide in water (A) and a 20% v/v TFE/water (B) solutio. The CT-NOE spectra recorded had zero amplitude modulation for 6.0 ad 7.9 Hz couplings. Negative intensity indicates a 3JN, coupling lower than the value shown on the left, positive intensity indicates a 3JNa coupling higher than the value shown on the left.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (1995, 374, 117-121) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20112333 K.Watanabe, S.Negi, Y.Sugiura, A.Kiriyama, A.Honbo, K.Iga, E.N.Kodama, T.Naitoh, M.Matsuoka, and K.Kano (2010).
Binding of multivalent anionic porphyrins to V3 loop fragments of an HIV-1 envelope and their antiviral activity.
  Chem Asian J, 5, 825-834.  
20923564 M.Masso, and I.I.Vaisman (2010).
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage.
  BMC Bioinformatics, 11, 494.  
19281264 A.Mor, E.Segal, B.Mester, B.Arshava, O.Rosen, F.X.Ding, J.Russo, A.Dafni, F.Schvartzman, T.Scherf, F.Naider, and J.Anglister (2009).
Mimicking the structure of the V3 epitope bound to HIV-1 neutralizing antibodies.
  Biochemistry, 48, 3288-3303.  
18366016 D.Katagiri, H.Fuji, S.Neya, and T.Hoshino (2008).
Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation.
  J Comput Chem, 29, 1930-1944.  
18594881 S.Q.Liu, S.X.Liu, and Y.X.Fu (2008).
Molecular motions of human HIV-1 gp120 envelope glycoproteins.
  J Mol Model, 14, 857-870.  
18039027 A.F.Poon, F.I.Lewis, S.L.Pond, and S.D.Frost (2007).
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.
  PLoS Comput Biol, 3, e231.  
16721558 K.B.Napier, Z.X.Wang, S.C.Peiper, and J.O.Trent (2007).
CCR5 interactions with the variable 3 loop of gp120.
  J Mol Model, 13, 29-41.  
17131136 S.Q.Liu, S.X.Liu, and Y.X.Fu (2007).
Dynamic domains and geometrical properties of HIV-1 gp120 during conformational changes induced by CD4 binding.
  J Mol Model, 13, 411-424.  
17212787 M.Levy, N.Garmy, E.Gazit, and J.Fantini (2006).
The minimal amyloid-forming fragment of the islet amyloid polypeptide is a glycolipid-binding domain.
  FEBS J, 273, 5724-5735.  
16731948 R.L.Stanfield, M.K.Gorny, S.Zolla-Pazner, and I.A.Wilson (2006).
Crystal structures of human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 2219 in complex with three different V3 peptides reveal a new binding mode for HIV-1 cross-reactivity.
  J Virol, 80, 6093-6105.
PDB codes: 2b0s 2b1a 2b1h
15725757 O.Hartley, P.J.Klasse, Q.J.Sattentau, and J.P.Moore (2005).
V3: HIV's switch-hitter.
  AIDS Res Hum Retroviruses, 21, 171-189.  
16379605 P.B.Gilbert, V.Novitsky, and M.Essex (2005).
Covariability of selected amino acid positions for HIV type 1 subtypes C and B.
  AIDS Res Hum Retroviruses, 21, 1016-1030.  
14962380 R.L.Stanfield, M.K.Gorny, C.Williams, S.Zolla-Pazner, and I.A.Wilson (2004).
Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D.
  Structure, 12, 193-204.
PDB code: 1q1j
15103622 S.T.Hsu, and A.M.Bonvin (2004).
Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120.
  Proteins, 55, 582-593.  
11322882 W.F.Vranken, F.Fant, M.Budesinsky, and F.A.Borremans (2001).
Conformational model for the consensus V3 loop of the envelope protein gp120 of HIV-1 in a 20% trifluoroethanol/water solution.
  Eur J Biochem, 268, 2620-2628.  
10985765 X.Zhu, C.Borchers, R.J.Bienstock, and K.B.Tomer (2000).
Mass spectrometric characterization of the glycosylation pattern of HIV-gp120 expressed in CHO cells.
  Biochemistry, 39, 11194-11204.  
  10438838 T.Murakami, T.Y.Zhang, Y.Koyanagi, Y.Tanaka, J.Kim, Y.Suzuki, S.Minoguchi, H.Tamamura, M.Waki, A.Matsumoto, N.Fujii, H.Shida, J.A.Hoxie, S.C.Peiper, and N.Yamamoto (1999).
Inhibitory mechanism of the CXCR4 antagonist T22 against human immunodeficiency virus type 1 infection.
  J Virol, 73, 7489-7496.  
10226501 Z.H.Peng (1999).
Solid phase synthesis and NMR conformational studies on cyclic decapeptide template molecule.
  Biopolymers, 49, 565-574.  
  8939697 S.E.O'Connor, and B.Imperiali (1996).
Modulation of protein structure and function by asparagine-linked glycosylation.
  Chem Biol, 3, 803-812.  
8617252 W.F.Vranken, M.Budesinsky, J.C.Martins, F.Fant, K.Boulez, H.Gras-Masse, and F.A.Borremans (1996).
Conformational features of a synthetic cyclic peptide corresponding to the complete V3 loop of the RF HIV-1 strain in water and water/trifluoroethanol solutions.
  Eur J Biochem, 236, 100-108.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.