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PDBsum entry 2gof
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Viral protein PDB id
2gof

 

 

 

 

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Contents
Protein chain
19 a.a.
PDB id:
2gof
Name: Viral protein
Title: Three-dimensional structure of the trans-membrane domain of vpu from HIV-1 in aligned phospholipid bicelles
Structure: Vpu protein. Chain: a. Fragment: trans-membrane domain, residues 2-30. Synonym: u orf protein. Engineered: yes. Mutation: yes
Source: Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: vpu. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 21 models
Authors: S.H.Park,A.A.De Angelis,A.A.Nevzorov,C.H.Wu,S.J.Opella
Key ref: S.H.Park et al. (2006). Three-dimensional structure of the transmembrane domain of Vpu from HIV-1 in aligned phospholipid bicelles. Biophys J, 91, 3032-3042. PubMed id: 16861273
Date:
12-Apr-06     Release date:   08-Aug-06    
PROCHECK
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 Headers
 References

Protein chain
Q70625  (VPU_HV1LW) -  Protein Vpu from Human immunodeficiency virus type 1 group M subtype B (isolate LW123)
Seq:
Struc: 		81 a.a.
19 a.a.
Key:    Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Biophys J 91:3032-3042 (2006)
PubMed id: 16861273  
 
 
Three-dimensional structure of the transmembrane domain of Vpu from HIV-1 in aligned phospholipid bicelles.
S.H.Park, A.A.De Angelis, A.A.Nevzorov, C.H.Wu, S.J.Opella.
 
  ABSTRACT  
 
The three-dimensional backbone structure of the transmembrane domain of Vpu from HIV-1 was determined by solid-state NMR spectroscopy in two magnetically-aligned phospholipid bilayer environments (bicelles) that differed in their hydrophobic thickness. Isotopically labeled samples of Vpu(2-30+), a 36-residue polypeptide containing residues 2-30 from the N-terminus of Vpu, were incorporated into large (q = 3.2 or 3.0) phospholipid bicelles composed of long-chain ether-linked lipids (14-O-PC or 16-O-PC) and short-chain lipids (6-O-PC). The protein-containing bicelles are aligned in the static magnetic field of the NMR spectrometer. Wheel-like patterns of resonances characteristic of tilted transmembrane helices were observed in two-dimensional (1)H/(15)N PISEMA spectra of uniformly (15)N-labeled Vpu(2-30+) obtained on bicelle samples with their bilayer normals aligned perpendicular or parallel to the direction of the magnetic field. The NMR experiments were performed at a (1)H resonance frequency of 900 MHz, and this resulted in improved data compared to lower-resonance frequencies. Analysis of the polarity-index slant-angle wheels and dipolar waves demonstrates the presence of a transmembrane alpha-helix spanning residues 8-25 in both 14-O-PC and 16-O-PC bicelles, which is consistent with results obtained previously in micelles by solution NMR and mechanically aligned lipid bilayers by solid-state NMR. The three-dimensional backbone structures were obtained by structural fitting to the orientation-dependent (15)N chemical shift and (1)H-(15)N dipolar coupling frequencies. Tilt angles of 30 degrees and 21 degrees are observed in 14-O-PC and 16-O-PC bicelles, respectively, which are consistent with the values previously determined for the same polypeptide in mechanically-aligned DMPC and DOPC bilayers. The difference in tilt angle in C14 and C16 bilayer environments is also consistent with previous results indicating that the transmembrane helix of Vpu responds to hydrophobic mismatch by changing its tilt angle. The kink found in the middle of the helix in the longer-chain C18 bilayers aligned on glass plates was not found in either of these shorter-chain (C14 or C16) bilayers.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21420337 D.T.Murray, Y.Lu, T.A.Cross, and J.R.Quine (2011).
Geometry of kinked protein helices from NMR data.
  J Magn Reson, 210, 82-89.  
21316275 G.J.Lu, W.S.Son, and S.J.Opella (2011).
A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.
  J Magn Reson, 209, 195-206.  
20951674 S.Tapaneeyakorn, A.D.Goddard, J.Oates, C.L.Willis, and A.Watts (2011).
Solution- and solid-state NMR studies of GPCRs and their ligands.
  Biochim Biophys Acta, 1808, 1462-1475.  
20858517 A.Andrew, and K.Strebel (2010).
HIV-1 Vpu targets cell surface markers CD4 and BST-2 through distinct mechanisms.
  Mol Aspects Med, 31, 407-417.  
20669237 J.X.Lu, S.Sharpe, R.Ghirlando, W.M.Yau, and R.Tycko (2010).
Oligomerization state and supramolecular structure of the HIV-1 Vpu protein transmembrane segment in phospholipid bilayers.
  Protein Sci, 19, 1877-1896.  
20334357 R.Soong, P.E.Smith, J.Xu, K.Yamamoto, S.C.Im, L.Waskell, and A.Ramamoorthy (2010).
Proton-evolved local-field solid-state NMR studies of cytochrome b5 embedded in bicelles, revealing both structural and dynamical information.
  J Am Chem Soc, 132, 5779-5788.  
19248817 A.Diller, C.Loudet, F.Aussenac, G.Raffard, S.Fournier, M.Laguerre, A.Grélard, S.J.Opella, F.M.Marassi, and E.J.Dufourc (2009).
Bicelles: A natural 'molecular goniometer' for structural, dynamical and topological studies of molecules in membranes.
  Biochimie, 91, 744-751.  
19929170 A.Tokarev, M.Skasko, K.Fitzpatrick, and J.Guatelli (2009).
Antiviral activity of the interferon-induced cellular protein BST-2/tetherin.
  AIDS Res Hum Retroviruses, 25, 1197-1210.  
19009593 J.Lee, S.Ham, and W.Im (2009).
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance.
  J Comput Chem, 30, 1334-1343.  
19496166 W.Im, J.Lee, T.Kim, and H.Rui (2009).
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.
  J Comput Chem, 30, 1622-1633.  
17827234 A.E.Daily, D.V.Greathouse, P.C.van der Wel, and R.E.Koeppe (2008).
Helical distortion in tryptophan- and lysine-anchored membrane-spanning alpha-helices as a function of hydrophobic mismatch: a solid-state deuterium NMR investigation using the geometric analysis of labeled alanines method.
  Biophys J, 94, 480-491.  
18177734 M.Musial-Siwek, D.A.Kendall, and P.L.Yeagle (2008).
Solution NMR of signal peptidase, a membrane protein.
  Biochim Biophys Acta, 1778, 937-944.  
18492613 S.H.Park, C.Loudet, F.M.Marassi, E.J.Dufourc, and S.J.Opella (2008).
Solid-state NMR spectroscopy of a membrane protein in biphenyl phospholipid bicelles with the bilayer normal parallel to the magnetic field.
  J Magn Reson, 193, 133-138.  
17947974 A.A.De Angelis, and S.J.Opella (2007).
Bicelle samples for solid-state NMR of membrane proteins.
  Nat Protoc, 2, 2332-2338.  
17216304 A.A.Nevzorov, S.H.Park, and S.J.Opella (2007).
Three-dimensional experiment for solid-state NMR of aligned protein samples in high field magnets.
  J Biomol NMR, 37, 113-116.  
17719813 C.V.Grant, S.L.Sit, A.A.De Angelis, K.S.Khuong, C.H.Wu, L.A.Plesniak, and S.J.Opella (2007).
An efficient (1)H/(31)P double-resonance solid-state NMR probe that utilizes a scroll coil.
  J Magn Reson, 188, 279-284.  
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.

 

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