2HYN

Complete ensemble of NMR structures of unphosphorylated human phospholamban pentamer


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 184 
  • Conformers Submitted: 184 
  • Selection Criteria: All calculated structures were submitted. Our method guarantees that the ensemble represents all structures that satisfy the data and have good vdW packing within a user-defined similarity level (chosen as 1 A). 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing.

Potluri, S.Yan, A.K.Chou, J.J.Donald, B.R.Bailey-Kellogg, C.

(2006) Proteins 65: 203-219

  • DOI: 10.1002/prot.21091

  • PubMed 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 dete ...

    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.


    Related Citations: 
    • The structure of phospholamban pentamer reveals a channel-like architecture in membranes
      Oxenoid, K.,Chou, J.J.
      (2005) Proc.Natl.Acad.Sci.USA 102: 10870


    Organizational Affiliation

    Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cardiac phospholamban
A, B, C, D, E
52Homo sapiensMutation(s): 0 
Gene Names: PLN (PLB)
Find proteins for P26678 (Homo sapiens)
Go to Gene View: PLN
Go to UniProtKB:  P26678
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 184 
  • Conformers Submitted: 184 
  • Selection Criteria: All calculated structures were submitted. Our method guarantees that the ensemble represents all structures that satisfy the data and have good vdW packing within a user-defined similarity level (chosen as 1 A). 
  • Olderado: 2HYN Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance