1QM8 | pdb_00001qm8

Structure of Bacteriorhodopsin at 100 K


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1QM8

This is version 2.2 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 Biology 283: 463

  • DOI: https://doi.org/10.1006/jmbi.1998.2103
  • Primary Citation 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 31.34 kDa 
  • Atom Count: 2,039 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BACTERIORHODOPSIN248Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan: G59827MO
GlyCosmos: G59827MO

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L3P

Query on L3P



Download:Ideal Coordinates CCD File
F [auth A]2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
L4P

Query on L4P



Download:Ideal Coordinates CCD File
G [auth A]3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N
L1P

Query on L1P



Download:Ideal Coordinates CCD File
D [auth A]3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
C43 H89 O6 P
UKQGAMWGTOTQPC-ALOLAALWSA-N
L2P

Query on L2P



Download:Ideal Coordinates CCD File
E [auth A],
H [auth A]
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
RET

Query on RET



Download:Ideal Coordinates CCD File
C [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.251 (Depositor) 
  • R-Value Observed: 0.251 (Depositor) 
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
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-09
    Changes: Structure summary