1KFZ

Solution Structure of C-terminal Sem-5 SH3 Domain (Ensemble of 16 Structures)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 16 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Solution Structure, Dynamics and Thermodynamics of the Native State Ensemble of Sem-5 C-Terminal SH3 Domain

Ferreon, J.C.Volk, D.E.Luxon, B.A.Gorenstein, D.Hilser, V.J.

(2003) Biochemistry 42: 5582-5591

  • DOI: https://doi.org/10.1021/bi030005j
  • Primary Citation of Related Structures:  
    1K76, 1KFZ

  • PubMed Abstract: 

    Although the high-resolution structure of a protein may provide significant insight into which regions are important for function, it is well-known that proteins undergo significant conformational fluctuations, even under native conditions. This suggests that the static structure alone may not provide sufficient information for elucidation of the thermodynamic determinants of biological function and that an accurate molecular-level description of function requires knowledge of the nature and energetics of the conformational states that constitute the native state ensemble. Here the native state ensemble of the C-terminal src homology domain-3 (C-SH3) from Caenorhabditis elegans Sem-5 has been studied using a variety of high-resolution biophysical techniques. In addition to determining the first solution structure of the unliganded protein, we have performed (15)N relaxation and native state hydrogen-deuterium exchange. It is observed that the regions of greatest structural variabilility also show low protection and order parameters, suggesting a higher degree of conformational diversity. These flexible regions also coincide with those regions of Sem-5 that have been predicted by the COREX algorithm to be unfolded in many of the most probable conformational states within the native state ensemble. The implications of this agreement and the potential role of conformational heterogeneity of the observed biophysical properties are discussed.


  • Organizational Affiliation

    Department of Human Biological Chemistry and Genetics and Sealy Center for Structural Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1055, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SEX MUSCLE ABNORMAL PROTEIN 562Caenorhabditis elegansMutation(s): 1 
Gene Names: Sem-5
UniProt
Find proteins for P29355 (Caenorhabditis elegans)
Explore P29355 
Go to UniProtKB:  P29355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29355
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 16 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection