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PDBsum entry 2hyn

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protein Protein-protein interface(s) links
Membrane protein/signaling protein PDB id
2hyn
Jmol
Contents
Protein chains
52 a.a.
PDB id:
2hyn
Name: Membrane protein/signaling protein
Title: Complete ensemble of nmr structures of unphosphorylated human phospholamban pentamer
Structure: Cardiac phospholamban. Chain: a, b, c, d, e. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pln. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 184 models
Authors: S.Potluri,A.K.Yan,J.J.Chou,B.R.Donald,C.Bailey-Kellogg
Key ref:
S.Potluri et al. (2006). Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. Proteins, 65, 203-219. PubMed id: 16897780 DOI: 10.1002/prot.21091
Date:
07-Aug-06     Release date:   29-Aug-06    
PROCHECK
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 Headers
 References

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     vesicle   12 terms 
  Biological process     regulation of cardiac muscle cell contraction   33 terms 
  Biochemical function     enzyme inhibitor activity     6 terms  

 

 
DOI no: 10.1002/prot.21091 Proteins 65:203-219 (2006)
PubMed id: 16897780  
 
 
Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing.
S.Potluri, A.K.Yan, J.J.Chou, B.R.Donald, C.Bailey-Kellogg.
 
  ABSTRACT  
 
Structural studies of symmetric homo-oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo-oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible conformations, and data-driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Completeness ensures that the algorithm does not miss the native conformation, and being data-driven enables it to assess the structural precision possible from data alone. Our algorithm performs a branch-and-bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible C(n) homo-oligomeric complexes for a given subunit structure. It eliminates those symmetry axes inconsistent with intersubunit nuclear Overhauser effect (NOE) distance restraints and then identifies conformations representing any consistent, well-packed structure to within a user-defined similarity level.For the human phospholamban pentamer in dodecylphosphocholine micelles, using the structure of one subunit determined from a subset of the experimental NMR data, our algorithm identifies a diverse set of complex structures consistent with the nine intersubunit NOE restraints. The distribution of determined structures provides an objective characterization of structural uncertainty: backbone RMSD to the previously determined structure ranges from 1.07 to 8.85 A, and variance in backbone atomic coordinates is an average of 12.32 A(2). Incorporating vdW packing reduces structural diversity to a maximum backbone RMSD of 6.24 A and an average backbone variance of 6.80 A(2). By comparing data consistency and packing quality under different assumptions of oligomeric number, our algorithm identifies the pentamer as the most likely oligomeric state of phospholamban, demonstrating that it is possible to determine the oligomeric number directly from NMR data. Additional tests on a number of homo-oligomers, from dimer to heptamer, similarly demonstrate the power of our method to provide unbiased determination and evaluation of homo-oligomeric complex structures.
 
  Selected figure(s)  
 
Figure 10.
Figure 10. The spread of simulated restraints across the first two chains in the reference structure of (a) Kv1.2 potassium channel (1QDV) and (b) haemagglutinin (1HTM). The red and blue segments indicate the first two chains, with the green lines indicating the restraints. The red and blue balls are the atoms on the chains between which the restraints exist.
Figure 11.
Figure 11. Histogram of backbone RMSD to the reference structure for the WPS structures returned by our approach for (a) human glycophorin A (dimer:1AFO), (b) influenza haemagglutinin (trimer:1HTM), (c) Kv1.2 potassium channel (tetramer:1QDV), and (d) Gp31 co-chaperonin (heptamer:1G31).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 203-219) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21036868 P.W.Rose, B.Beran, C.Bi, W.F.Bluhm, D.Dimitropoulos, D.S.Goodsell, A.Prlic, M.Quesada, G.B.Quinn, J.D.Westbrook, J.Young, B.Yukich, C.Zardecki, H.M.Berman, and P.E.Bourne (2011).
The RCSB Protein Data Bank: redesigned web site and web services.
  Nucleic Acids Res, 39, D392-D401.  
18951392 B.Bardiaux, A.Bernard, W.Rieping, M.Habeck, T.E.Malliavin, and M.Nilges (2009).
Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA.
  Proteins, 75, 569-585.  
19711185 J.Zeng, J.Boyles, C.Tripathy, L.Wang, A.Yan, P.Zhou, and B.R.Donald (2009).
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
  J Biomol NMR, 45, 265-281.
PDB code: 2kiq
18365752 M.S.Apaydin, V.Conitzer, and B.R.Donald (2008).
Structure-based protein NMR assignments using native structural ensembles.
  J Biomol NMR, 40, 263-276.  
18212017 T.E.Williamson, B.A.Craig, E.Kondrashkina, C.Bailey-Kellogg, and A.M.Friedman (2008).
Analysis of self-associating proteins by singular value decomposition of solution scattering data.
  Biophys J, 94, 4906-4923.  
18436958 X.Wang, S.Bansal, M.Jiang, and J.H.Prestegard (2008).
RDC-assisted modeling of symmetric protein homo-oligomers.
  Protein Sci, 17, 899-907.  
17192589 S.Potluri, A.K.Yan, B.R.Donald, and C.Bailey-Kellogg (2007).
A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers.
  Protein Sci, 16, 69-81.  
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 code is shown on the right.