1QM8

Structure of Bacteriorhodopsin at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies.

Takeda, K.Sato, H.Hino, T.Kono, M.Fukuda, K.Sakurai, I.Okada, T.Kouyama, T.

(1998) J Mol Biol 283: 463

  • DOI: 10.1006/jmbi.1998.2103
  • Primary Citation of Related Structures:  
    1QM8

  • PubMed Abstract: 
  • When the two-dimensional crystal of bacteriorhodopsin (bR), purple membrane, is incubated at high temperature (32 degreesC) with a small amount of the neutral detergent octylthioglucoside in the presence of the precipitant ammonium sulfate, a large fraction of the membrane fragments is converted into spherical vesicles with a diameter of 50 nm, which are able to assemble into optically isotropic hexagonal crystals when the precipitant concentration is increased ...

    When the two-dimensional crystal of bacteriorhodopsin (bR), purple membrane, is incubated at high temperature (32 degreesC) with a small amount of the neutral detergent octylthioglucoside in the presence of the precipitant ammonium sulfate, a large fraction of the membrane fragments is converted into spherical vesicles with a diameter of 50 nm, which are able to assemble into optically isotropic hexagonal crystals when the precipitant concentration is increased. The vesicularization of purple membrane takes place under such a condition that the miscibility of the detergent to the aqueous phase becomes very low, and we suggest that it is initiated by insertion of the detergent molecules into the membrane. At low temperature, the transformation into the vesicular structure is inhibited and no large crystal is produced directly from membrane/detergent/precipitant mixtures. When a suspension of the spherical vesicles produced at the high temperature is cooled and concentrated below 15 degreesC, however, a birefringent hexagonal crystal is produced that diffracts X-rays beyond 2.5 A resolution. This new crystal belongs to the space group P622 with unit cell dimensions of a=b=104.7 A and c=114.1 A, and it is shown to be made up of stacked planar membranes, in each of which the bR trimers are arranged on a honeycomb lattice and the space among the proteins is filled with the detergent molecules and native lipids. These stacked membranes are suggested to be produced by successive fusion of the spherical vesicles. This implies that the crystallization is achieved without any step for complete solubilization of the protein. The present result offers a unique crystallization method that may be applicable to such membrane proteins that are liable to denature in the presence of an excess amount of detergent.


    Related Citations: 
    • Specific Lipid-Protein Interactions in a Novel Honeycomb Lattice Structure of Bacteriorhodopsin
      Sato, H., Takeda, K., Tani, K., Hino, T., Okada, T., Nakasako, M., Kamiya, N., Kouyama, T.
      (1999) Acta Crystallogr D Biol Crystallogr D55: 1251

    Organizational Affiliation

    Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIORHODOPSIN A248Halobacterium salinarumMutation(s): 0 
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose
B
3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L3P
Query on L3P

Download Ideal Coordinates CCD File 
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
L4P
Query on L4P

Download Ideal Coordinates CCD File 
A
3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N
 Ligand Interaction
L1P
Query on L1P

Download Ideal Coordinates CCD File 
A
3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
C43 H89 O6 P
UKQGAMWGTOTQPC-ALOLAALWSA-N
 Ligand Interaction
L2P
Query on L2P

Download Ideal Coordinates CCD File 
A
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
RET
Query on RET

Download Ideal Coordinates CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.1α = 90
b = 102.1β = 90
c = 112.3γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary