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 1.4 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: https://doi.org/10.1002/prot.21091
  • Primary Citation of Related Structures:  
    2HYN

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cardiac phospholamban
A, B, C, D, E
52Homo sapiensMutation(s): 0 
Gene Names: PLN
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P26678 (Homo sapiens)
Explore P26678 
Go to UniProtKB:  P26678
PHAROS:  P26678
GTEx:  ENSG00000198523 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26678
Sequence Annotations
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  • Reference Sequence
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). 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection