7JRI

High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle, 33 ms structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

High-resolution crystal structures of transient intermediates in the phytochrome photocycle.

Carrillo, M.Pandey, S.Sanchez, J.Noda, M.Poudyal, I.Aldama, L.Malla, T.N.Claesson, E.Wahlgren, W.Y.Feliz, D.Srajer, V.Maj, M.Castillon, L.Iwata, S.Nango, E.Tanaka, R.Tanaka, T.Fangjia, L.Tono, K.Owada, S.Westenhoff, S.Stojkovic, E.A.Schmidt, M.

(2021) Structure 29: 743

  • DOI: https://doi.org/10.1016/j.str.2021.03.004
  • Primary Citation of Related Structures:  
    7JR5, 7JRI

  • PubMed Abstract: 

    Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting Pr state and the light-activated Pfr state. Light signals are transduced as structural change through the entire protein to modulate its activity. It is unknown how the Pr-to-Pfr interconversion occurs, as the structure of intermediates remains notoriously elusive. Here, we present short-lived crystal structures of the photosensory core modules of the bacteriophytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray free electron laser 5 ns and 33 ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway that extends through the entire protein. The snapshots show with atomic precision how the signal progresses from the chromophore, explaining how plants, bacteria, and fungi sense red light.


  • Organizational Affiliation

    Department of Biology, Northeastern Illinois University, 5500 North St. Louis Avenue, Chicago, IL 60625, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photoreceptor-histidine kinase BphP
A, B
482Stigmatella aurantiacaMutation(s): 0 
Gene Names: STIAU_8420
EC: 2.7.13.3
UniProt
Find proteins for Q09E27 (Stigmatella aurantiaca (strain DW4/3-1))
Explore Q09E27 
Go to UniProtKB:  Q09E27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09E27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3Q8 (Subject of Investigation/LOI)
Query on 3Q8

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
3-[2-[[5-[[(3E,4S)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
C33 H40 N4 O6
YHFJLIYOVARRSS-AYZAYIPBSA-N
BEN
Query on BEN

Download Ideal Coordinates CCD File 
D [auth B]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.69α = 90
b = 83.4β = 107.63
c = 86.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-1231306

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary