8QI8

Cryogenic temperature dark state structure of CrPhotLOV1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography.

Gotthard, G.Mous, S.Weinert, T.Maia, R.N.A.James, D.Dworkowski, F.Gashi, D.Furrer, A.Ozerov, D.Panepucci, E.Wang, M.Schertler, G.F.X.Heberle, J.Standfuss, J.Nogly, P.

(2024) IUCrJ 11: 792-808

  • DOI: https://doi.org/10.1107/S2052252524005608
  • Primary Citation of Related Structures:  
    8QI8, 8QI9, 8QIA, 8QIB, 8QIF, 8QIG, 8QIH, 8QII, 8QIK, 8QIL, 8QIM, 8QIN, 8QIO, 8QIP, 8QIQ, 8QIR, 8QIS, 8QIT, 8QIU, 8QIV, 8QIW

  • PubMed Abstract: 

    Light-oxygen-voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.


  • Organizational Affiliation

    Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phototropin118Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PHOT
UniProt
Find proteins for Q8LPD9 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q8LPD9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.09α = 90
b = 121.09β = 90
c = 46.04γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union701647
Swiss National Science FoundationSwitzerlandPZ00P3_174169
Polish National Science CentrePolandUMO-2021/03/H/NZ1/00002
Swiss National Science FoundationSwitzerland192760

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references
  • Version 1.2: 2024-09-11
    Changes: Database references