2Y6N

STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Membrane Protein Crystallization in Lipidic Mesophases. Hosting Lipid Effects on the Crystallization and Structure of a Transmembrane Peptide

Hoefer, N.Aragao, D.Lyons, J.Caffrey, M.

(2011) Cryst.Growth Des. 11: 1182

  • DOI: 10.1021/cg101384p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gramicidin is an apolar pentadecapeptide antibiotic consisting of alternating D-and L-amino acids. It functions, in part, by creating pores in membranes of susceptible cells rendering them leaky to monovalent cations. The peptide should be able to tr ...

    Gramicidin is an apolar pentadecapeptide antibiotic consisting of alternating D-and L-amino acids. It functions, in part, by creating pores in membranes of susceptible cells rendering them leaky to monovalent cations. The peptide should be able to traverse the host membrane either as a double stranded, intertwined double helix (DSDH) or as a head-to-head single stranded helix (HHSH). Current structure models are based on macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR). However, the HHSH form has only been observed by NMR. The shape and size of the different gramicidin conformations differ. We speculated therefore that reconstituting it into a lipidic mesophase with bilayers of different microstructures would preferentially stabilize one form over the other. By using such mesophases for in meso crystallogenesis the expectation was that at least one would generate crystals of gramicidin in the HHSH form for structure determination by MX. This was tested using commercial and in-house synthesised lipids that support in meso crystallogenesis. Lipid acyl chain lengths were varied from 14 to 18 carbons to provide mesophases with a range of bilayer thicknesses. Unexpectedly, all lipids produced high quality, structure-grade crystals with gramicidin only in the DSDH conformation.


    Organizational Affiliation

    Membrane Structural and Functional Biology Group, School of Biochemistry and Immunology, and School of Medicine, Trinity College, Dublin.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VAL-GRAMICIDIN A
A, B, C, D, E, F
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download SDF File 
Download CCD File 
A, D
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
P4C
Query on P4C

Download SDF File 
Download CCD File 
A
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
POLYETHYLENE 400
C14 H28 O8
CTLLATPOKUEFSQ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000150
Query on PRD_000150
A,B,C,D,E,FGRAMICIDIN APolypeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 30.616α = 90.00
b = 62.783β = 100.02
c = 30.602γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-07-24
    Type: Other
  • Version 1.3: 2014-01-15
    Type: Database references, Version format compliance
  • Version 1.4: 2019-03-06
    Type: Data collection, Derived calculations, Experimental preparation, Other