6G7L | pdb_00006g7l

Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 8.3 ms state structure

• PDB DOI: https://doi.org/10.2210/pdb6G7L/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halobacterium salinarum NRC-1
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-04-06 Released: 2018-06-27 
• Deposition Author(s): Nogly, P., Weinert, T., James, D., Cabajo, 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., Bruenle, 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.
• Funding Organization(s): Swiss National Science Foundation, European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 29903883 
• DOI: https://doi.org/10.1126/science.aat0094
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.
Photon Science Division-Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland.
Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Science IT, Paul Scherrer Institut, 5232 Villigen, Switzerland.
SwissFEL, Paul Scherrer Institut, 5232 Villigen, Switzerland.
Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden.
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe- cho, Sakyo-ku, Kyoto 606-8501, Japan.
Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland. [e-mail].

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 (software)

Macromolecule Content 

• Total Structure Weight: 34.45 kDa 
• Atom Count: 2,039 
• Modeled Residue Count: 230 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	262	Halobacterium salinarum NRC-1	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LI1	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL C42 H86 O3 YERVUJAKCNBGCR-BIHSMRAKSA-N
OLC	J [auth A], K [auth A], L [auth A], M [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-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:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.32	α = 90
b = 62.32	β = 90
c = 111.1	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Nogly, P., Weinert, T., James, D., Cabajo, 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., Bruenle, 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.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_159558
Swiss National Science Foundation	Switzerland	310030_153145
Swiss National Science Foundation	Switzerland	PZ00P3_174169
European Commission	Switzerland	290605

Revision History  

• 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
• Version 1.4: 2024-10-16
  Changes: Structure summary