1GRM

REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Refinement of the Spatial Structure of the Gramicidin a Ion Channel

Lomize, A.L.Orekhov, V.I.U.Arsen'Ev, A.S.

(1992) Biol.Membr.(Ussr) 18: 182


  • PubMed Abstract: 
  • The spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cros ...

    The spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cross-peak volumes with those calculated for low-energy GA conformations, dynamic averaging of the low-energy conformation set and restrained energy minimization. Accuracy of the spatial structure determination was estimated by the penalty function Fr defined as a root mean square deviation of interproton distances corresponding to the calculated and experimental cross-peak volumes. As the initial conformation we used the right-handed pi 6,3 LD pi 6,3 LD helix established on the base of NMR data regardless of the cross-peak volumes. The conformation is in a good agreement with NOE cross-peak volumes (Fr 0.2 to 0.5 A depending on NOESY spectrum). For a number of NOEs formed by the side chain protons, distances errors were found as much as 0.5-2.0 A. Restrained energy minimization procedure had little further success. However some of these errors were eliminated by the change in torsional angle chi 2 of D-Leu12 and dynamic averaging of the Val7 side chain conformations. Apparently, majority of deviations of the calculated and experimental cross-peak volumes are due to the intramolecular mobility of GA and cannot be eliminated within the framework of rigid globule model. In summary the spatial structure of GA ion-channel can be thought as a set of low-energy conformations, differing by the side chain torsion angles chi 1 Val7 and chi 2 D-Leu4 and D-Leu10 and the orientation of the C-terminal ethanolamine group. Root mean square differences between the atomic coordinates of conformations are in the range of 0.3-0.8 A.


    Related Citations: 
    • 1H-NMR Study of Gramicidin a Transmembrane Ion Channel. Head-to-Head Right-Handed, Single-Stranded Helices.
      Arseniev, A.S.,Barsukov, I.L.,Bystrov, V.F.,Lomize, A.L.,Ovchinnikov, Yu.A.
      (1985) FEBS Lett. 186: 168
    • Spatial Structure of Gramicidin a Transmembrane Ion Channel-NMR Analysis in Micelles (Russian)
      Arseniev, A.S.,Barsukov, I.L.,Bystrov, V.F.,Ovchinnikov, Yu.A.
      (1986) Biol.Membr.(Ussr) 3: 437
    • Gramicidin a Transmembrane Ion-Channel. Three-Dimensional Structure Reconstruction Based on NMR Spectroscopy and Energy Refinement (Russian)
      Arseniev, A.S.,Lomize, A.L.,Barsukov, I.L.,Bystrov, V.F.
      (1986) Biol.Membr.(Ussr) 3: 1077



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GRAMICIDIN A
A, B
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000150
Query on PRD_000150
A,BGRAMICIDIN APolypeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other
  • Version 1.5: 2017-12-20
    Type: Database references, Other