PAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps after photoexcitation

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.

Claesson, E.Wahlgren, W.Y.Takala, H.Pandey, S.Castillon, L.Kuznetsova, V.Henry, L.Panman, M.Carrillo, M.Kubel, J.Nanekar, R.Isaksson, L.Nimmrich, A.Cellini, A.Morozov, D.Maj, M.Kurttila, M.Bosman, R.Nango, E.Tanaka, R.Tanaka, T.Fangjia, L.Iwata, S.Owada, S.Moffat, K.Groenhof, G.A Stojkovic, E.A Ihalainen, J.Schmidt, M.Westenhoff, S.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.53514
  • Primary Citation of Related Structures:  
    6T3L, 6T3U

  • PubMed Abstract: 

    Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

  • Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BacteriophytochromeA [auth B],
B [auth A]
343Deinococcus radioduransMutation(s): 0 
Gene Names: bphPDR_A0050
Find proteins for Q9RZA4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RZA4 
Go to UniProtKB:  Q9RZA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RZA4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBV (Subject of Investigation/LOI)
Query on LBV

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid
C33 H37 N4 O6
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.98α = 90
b = 116.69β = 90
c = 117.86γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilSweden279944
Japan Agency for Medical Research and Development (AMED)Japan--
Academy of FinlandFinland285461
Academy of FinlandFinland296135

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Refinement description