2DCP

Fully automated NMR structure determination of the ENTH-VHS domain AT3G16270 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Automated Protein Structure Determination from NMR Spectra

Lopez-Mendez, B.Guntert, P.

(2006) J.Am.Chem.Soc. 128: 13112-13122

  • DOI: 10.1021/ja061136l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak ...

    Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus chemical shift assignments for all (1)H, (13)C, and (15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The three-dimensional structures of three 12-16 kDa proteins computed with the FLYA algorithm coincided closely with the conventionally determined structures. Deviations were below 0.95 A for the backbone atom positions, excluding the flexible chain termini. 96-97% of all backbone and side-chain chemical shifts in the structured regions were assigned to the correct residues. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.


    Related Citations: 
    • NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana
      Lopez-Mendez, B.,Pantoja-Uceda, D.,Tomizawa, T.,Koshiba, S.,Kigawa, T.,Shirouzu, M.,Terada, T.,Inoue, M.,Yabuki, T.,Aoki, M.,Seki, E.,Matsuda, T.,Hirota, H.,Yoshida, M.,Tanaka, A.,Osanai, T.,Seki, M.,Shinozaki, K.,Yokoyama, S.,Guntert, P.
      (2004) J.Biomol.NMR 29: 205


    Organizational Affiliation

    Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein (RAFL09-17-B18)
A
140Arabidopsis thalianaMutation(s): 0 
Gene Names: MTV1
Find proteins for Q9C5H4 (Arabidopsis thaliana)
Go to UniProtKB:  Q9C5H4
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 
  • Olderado: 2DCP Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance