Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation

Experimental Data Snapshot

  • Resolution: 1.33 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.136 

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Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin.

Taguchi, S.Niwa, S.Dao, H.A.Tanaka, Y.Takeda, R.Fukai, S.Hasegawa, K.Takeda, K.

(2023) Commun Biol 6: 190-190

  • DOI: https://doi.org/10.1038/s42003-023-04554-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The K intermediate of proton pumping bacteriorhodopsin is the first intermediate generated after isomerization of retinal to the 13-cis form. Although various structures have been reported for the K intermediate until now, these differ from each other, especially in terms of the conformation of the retinal chromophore and its interaction with surrounding residues. We report here an accurate X-ray crystallographic analysis of the K structure. The polyene chain of 13-cis retinal is observed to be S-shaped. The side chain of Lys216, which is covalently bound to retinal via the Schiff-base linkage, interacts with residues, Asp85 and Thr89. In addition, the Nζ-H of the protonated Schiff-base linkage interacts with a residue, Asp212 and a water molecule, W402. Based on quantum chemical calculations for this K structure, we examine the stabilizing factors of distorted conformation of retinal and propose a relaxation manner to the next L intermediate.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku, 606-8502, Japan. ktakeda@kuchem.kyoto-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin230Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L2P

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
C43 H88 O3
Query on SQU

Download Ideal Coordinates CCD File 
H [auth A],
R [auth A],
S [auth A],
T [auth A]
C27 H56
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
C20 H28 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.33 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.136 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.57α = 90
b = 60.57β = 90
c = 110.89γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release