Solution NMR structure of Dsy0195(21-82) protein from Desulfitobacterium Hafniense. Northeast Structural Genomics Consortium Target DhR8C

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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Combining NMR and EPR methods for homodimer protein structure determination.

Yang, Y.Ramelot, T.A.McCarrick, R.M.Ni, S.Feldmann, E.A.Cort, J.R.Wang, H.Ciccosanti, C.Jiang, M.Janjua, H.Acton, T.B.Xiao, R.Everett, J.K.Montelione, G.T.Kennedy, M.A.

(2010) J Am Chem Soc 132: 11910-11913

  • DOI: https://doi.org/10.1021/ja105080h
  • Primary Citation of Related Structures:  
    2KS0, 2KYI

  • PubMed Abstract: 

    There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 A. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
71Desulfitobacterium hafniense Y51Mutation(s): 0 
Gene Names: DSY0195
Find proteins for Q251Q8 (Desulfitobacterium hafniense (strain Y51))
Explore Q251Q8 
Go to UniProtKB:  Q251Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ251Q8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-05
    Changes: Data collection, Database references, Other
  • Version 1.3: 2023-06-14
    Changes: Database references, Other