1IW9

Crystal Structure of the M Intermediate of Bacteriorhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix

Takeda, K.Matsui, Y.Kamiya, N.Adachi, S.Okumura, H.Kouyama, T.

(2004) J.Mol.Biol. 341: 1023-1037

  • Primary Citation of Related Structures:  1DZE

  • PubMed Abstract: 
  • Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M int ...

    Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M intermediate by a factor of approximately 100,allowing high levels of the M intermediate to accumulate under continuous illumination. When the M intermediate generated at room temperature was exposed to a low flux of X-rays (approximately 10(14) photons/mm2), this yellow intermediate was converted into a blue species having an absorption maximum at 650 nm. This color change is suggested to accompany a configuration change in the retinal-Lys216 chain. The true conformational change associated with formation of the M intermediate was analyzed by taking the X-radiation-induced structural change into account. Our result indicates that, upon formation of the M intermediate, helix G move stowards the extra-cellular side by, on average, 0.5 angstroms. This movement is coupled with several reactions occurring at distal sites in the protein: (1) reorientation of the side-chain of Leu93 contacting the C13 methyl group of retinal, which is accompanied by detachment of a water molecule from the Schiff base; (2) a significant distortion in the F-G loop, triggering destruction of a hydrogen bonding interaction between a pair of glutamate groups (Glu194 and Glu204); (3) formation of a salt bridge between the carboxylate group of Glu204 and the guanidinium ion of Arg82, which is accompanied by a large distortion in the extra-cellular half of helix C; (4)noticeable movements of the AB loop and the cytoplasmic end of helix B. But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules.


    Related Citations: 
    • Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle
      Kouyama, T.,Nishikawa, T.,Tokuhisa, T.,Okumura, H.
      (2004) J.Mol.Biol. 335: 531


    Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
bacteriorhodopsin
A
248Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Gene Names: bop
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GAL
Query on GAL

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A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
RET
Query on RET

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Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
GLC
Query on GLC

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A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
L2P
Query on L2P

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A
2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
L3P
Query on L3P

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A
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.300α = 90.00
b = 102.300β = 90.00
c = 112.300γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSphasing
SCALAdata scaling
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance