Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.

Nogly, P.Weinert, T.James, D.Carbajo, S.Ozerov, D.Furrer, A.Gashi, D.Borin, V.Skopintsev, P.Jaeger, K.Nass, K.Bath, P.Bosman, R.Koglin, J.Seaberg, M.Lane, T.Kekilli, D.Brunle, S.Tanaka, T.Wu, W.Milne, C.White, T.Barty, A.Weierstall, U.Panneels, V.Nango, E.Iwata, S.Hunter, M.Schapiro, I.Schertler, G.Neutze, R.Standfuss, J.

(2018) Science 361

  • DOI: https://doi.org/10.1126/science.aat0094
  • Primary Citation of Related Structures:  
    6G7H, 6G7I, 6G7J, 6G7K, 6G7L

  • PubMed Abstract: 

    Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.

  • Organizational Affiliation

    Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin248Halobacterium salinarum NRC-1Mutation(s): 0 
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 LI1

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],
H [auth A],
I [auth A]
C42 H86 O3
Query on OLC

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on RET

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

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.32α = 90
b = 62.32β = 90
c = 111.1γ = 120
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_159558
Swiss National Science FoundationSwitzerland310030_153145
Swiss National Science FoundationSwitzerlandPZ00P3_174169
European CommissionSwitzerland290605

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-14
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description