TR-SMX closed state structure (0-5ms) of bacteriorhodopsin

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 

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Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography.

Weinert, T.Skopintsev, P.James, D.Dworkowski, F.Panepucci, E.Kekilli, D.Furrer, A.Brunle, S.Mous, S.Ozerov, D.Nogly, P.Wang, M.Standfuss, J.

(2019) Science 365: 61-65

  • DOI: https://doi.org/10.1126/science.aaw8634
  • Primary Citation of Related Structures:  
    6RNJ, 6RPH, 6RQO, 6RQP

  • PubMed Abstract: 

    Conformational dynamics are essential for proteins to function. We adapted time-resolved serial crystallography developed at x-ray lasers to visualize protein motions using synchrotrons. We recorded the structural changes in the light-driven proton-pump bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release at a quality comparable to that of previous x-ray laser experiments. From 10 to 15 milliseconds onwards, we observe large additional structural rearrangements up to 9 angstroms on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid-96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle.

  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zürich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin229Halobacterium 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

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

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 62β = 90
c = 110.3γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description