6G7J

Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 457-646 fs state structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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

    Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland. joerg.standfuss@psi.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BacteriorhodopsinA262Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI1
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]
1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
C42 H86 O3
YERVUJAKCNBGCR-BIHSMRAKSA-N
 Ligand Interaction
OLC
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
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • 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
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

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