1QHJ

X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES

• PDB DOI: https://doi.org/10.2210/pdb1QHJ/pdb

• Classification: PHOTORECEPTOR
• Organism(s): Halobacterium salinarum
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 1999-05-04 Released: 1999-07-21 
• Deposition Author(s): Belrhali, H., Nollert, P., Royant, A., Menzel, C., Rosenbusch, J.P., Landau, E.M., Pebay-Peyroula, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.224 

Literature

Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution.

Belrhali, H., Nollert, P., Royant, A., Menzel, C., Rosenbusch, J.P., Landau, E.M., Pebay-Peyroula, E.

(1999) Structure 7: 909-917

• PubMed: 10467143 
• DOI: https://doi.org/10.1016/s0969-2126(99)80118-x
• Primary Citation of Related Structures:  
  1QHJ


• PubMed Abstract: 
  

  Bacteriorhodopsin (bR) from Halobacterium salinarum is a proton pump that converts the energy of light into a proton gradient that drives ATP synthesis. The protein comprises seven transmembrane helices and in vivo is organized into purple patches, in which bR and lipids form a crystalline two-dimensional array. Upon absorption of a photon, retinal, which is covalently bound to Lys216 via a Schiff base, is isomerized to a 13-cis,15-anti configuration. This initiates a sequence of events - the photocycle - during which a proton is transferred from the Schiff base to Asp85, followed by proton release into the extracellular medium and reprotonation from the cytoplasmic side.

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Organizational Affiliation: 

ESRF, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 32.83 kDa 
• Atom Count: 2,203 
• Modelled Residue Count: 228 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (BACTERIORHODOPSIN)	A	248	Halobacterium salinarum	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PH1	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-[DI-2,6,10,14-TETRAMETHYL-HEXADECAN-16-OXY]-PROPANE C43 H88 O2 ICKFQWWHLUUVMF-FYYCEQFTSA-N
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.224 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.8	α = 90
b = 60.8	β = 90
c = 110.52	γ = 120

Software Package:

Software Name	Purpose
BASED	model building
CNS	refinement
XDS	data reduction
CCP4	data scaling
BASED	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-21 
Deposition Author(s): Belrhali, H., Nollert, P., Royant, A., Menzel, C., Rosenbusch, J.P., Landau, E.M., Pebay-Peyroula, E.

Revision History  

• Version 1.0: 1999-07-21
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description