9F9E

Laser excitation effects on BR: Extrapolated 6 ps Light dataset recorded at 342 GW/cm2 at SwissFEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate.

Bertrand, Q.Nogly, P.Nango, E.Kekilli, D.Khusainov, G.Furrer, A.James, D.Dworkowski, F.Skopintsev, P.Mous, S.Martiel, I.Borjesson, P.Ortolani, G.Huang, C.Y.Kepa, M.Ozerov, D.Brunle, S.Panneels, V.Tanaka, T.Tanaka, R.Tono, K.Owada, S.Johnson, P.J.M.Nass, K.Knopp, G.Cirelli, C.Milne, C.Schertler, G.Iwata, S.Neutze, R.Weinert, T.Standfuss, J.

(2024) Nat Commun 15: 10278-10278

  • DOI: https://doi.org/10.1038/s41467-024-54422-8
  • Primary Citation of Related Structures:  
    9F9B, 9F9C, 9F9D, 9F9E, 9F9F, 9F9G, 9F9H, 9F9I, 9F9J

  • PubMed Abstract: 

    Time-resolved serial crystallography at X-ray Free Electron Lasers offers the opportunity to observe ultrafast photochemical reactions at the atomic level. The technique has yielded exciting molecular insights into various biological processes including light sensing and photochemical energy conversion. However, to achieve sufficient levels of activation within an optically dense crystal, high laser power densities are often used, which has led to an ongoing debate to which extent photodamage may compromise interpretation of the results. Here we compare time-resolved serial crystallographic data of the bacteriorhodopsin K-intermediate collected at laser power densities ranging from 0.04 to 2493 GW/cm 2 and follow energy dissipation of the absorbed photons logarithmically from picoseconds to milliseconds. Although the effects of high laser power densities on the overall structure are small, in the upper excitation range we observe significant changes in retinal conformation and increased heating of the functionally critical counterion cluster. We compare light-activation within crystals to that in solution and discuss the impact of the observed changes on bacteriorhodopsin biology.


  • Organizational Affiliation

    Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin230Halobacterium salinarumMutation(s): 0 
Gene Names: bopVNG_1467G
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LI1
Query on LI1

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [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
Query on OLC

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET (Subject of Investigation/LOI)
Query on RET

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.259 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.95α = 90
b = 62.95β = 90
c = 111.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
InnosuisseEuropean Union42711.1 IP-LS

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release