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PDBsum entry 1pln

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protein Protein-protein interface(s) links
Membrane protein PDB id
1pln
Jmol
Contents
Protein chains
18 a.a.
Theoretical model
PDB id:
1pln
Name: Membrane protein
Title: Model of the pentameric transmembrane domain of phospholamban, a putative cardiac ion channel
Structure: Cardiac phospholamban. Chain: a, b, c, d, e. Fragment: putative membrane spanning domain 35-52. Synonym: plb(35-52)
Source: Homo sapiens. Human. Other_details: sarcoplasmic reticulum
Authors: P.Herzyk,R.E.Hubbard
Key ref: P.Herzyk and R.E.Hubbard (1998). Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban. Biophys J, 74, 1203-1214. PubMed id: 9512019
Date:
06-Aug-98     Release date:   12-Aug-98    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P26678  (PPLA_HUMAN) -  Cardiac phospholamban
Seq:
Struc:
52 a.a.
18 a.a.
Key:    PfamA domain  Secondary structure

 

 
Biophys J 74:1203-1214 (1998)
PubMed id: 9512019  
 
 
Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban.
P.Herzyk, R.E.Hubbard.
 
  ABSTRACT  
 
Molecular models of the transmembrane domain of the phospholamban pentamer have been generated by a computational method that uses the experimentally measured effects of systematic single-site mutations as a guiding force in the modeling procedure. This method makes the assumptions that 1) the phospholamban transmembrane domain is a parallel five-helix bundle, and 2) nondisruptive mutation positions are lipid exposed, whereas 3) disruptive or partially disruptive mutations are not. Our procedure requires substantially less computer time than systematic search methods, allowing rapid assessment of the effects of different experimental results on the helix arrangement. The effectiveness of the approach is investigated in test calculations on two helix-dimer systems of known structure. Two independently derived sets of mutagenesis data were used to define the restraints for generating models of phospholamban. Both resulting models are left-handed, highly symmetrical pentamers. Although the overall bundle geometry is very similar in the two models, the orientation of individual helices differs by approximately 50 degrees, resulting in different sets of residues facing the pore. This demonstrates how differences in restraints can have an effect on the model structures generated, and how the violation of these restraints can identify inconsistent experimental data.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17085501 L.Bu, W.Im, and C.L.Brooks (2007).
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.
  Biophys J, 92, 854-863.  
16531225 A.Sivasubramanian, G.Chao, H.M.Pressler, K.D.Wittrup, and J.J.Gray (2006).
Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis.
  Structure, 14, 401-414.
PDB codes: 2exp 2exq
15654870 A.D.van Dijk, R.Boelens, and A.M.Bonvin (2005).
Data-driven docking for the study of biomolecular complexes.
  FEBS J, 272, 293-312.  
15787961 A.M.Slovic, J.D.Lear, and W.F.DeGrado (2005).
De novo design of a pentameric coiled-coil: decoding the motif for tetramer versus pentamer formation in water-soluble phospholamban.
  J Pept Res, 65, 312-321.  
15768404 V.Nanda, and W.F.DeGrado (2005).
Automated use of mutagenesis data in structure prediction.
  Proteins, 59, 454-466.  
15382237 Y.Park, M.Elsner, R.Staritzbichler, and V.Helms (2004).
Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices.
  Proteins, 57, 577-585.  
11606268 P.Sompornpisut, Y.S.Liu, and E.Perozo (2001).
Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations.
  Biophys J, 81, 2530-2546.  
11256577 M.C.Peitsch, T.Schwede, and N.Guex (2000).
Automated protein modelling--the proteome in 3D.
  Pharmacogenomics, 1, 257-266.  
10096878 P.Pollesello, A.Annila, and M.Ovaska (1999).
Structure of the 1-36 amino-terminal fragment of human phospholamban by nuclear magnetic resonance and modeling of the phospholamban pentamer.
  Biophys J, 76, 1784-1795.  
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.