8R44 | pdb_00008r44

PAS-GAF bidomain of Glycine max phytochrome A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.195 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.186 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Pr and Pfr structures of plant phytochrome A.

Nagano, S.von Stetten, D.Guan, K.Chen, P.Y.Song, C.Barends, T.Weiss, M.S.Feiler, C.G.Dorner, K.de Diego Martinez, I.Schubert, R.Bielecki, J.Brings, L.Han, H.Kharitonov, K.Kim, C.Kloos, M.Koliyadu, J.C.P.Koua, F.H.M.Round, E.Sarma, A.Sato, T.Schmidt, C.Valerio, J.Wrona, A.Schulz, J.de Wijn, R.Letrun, R.Bean, R.Mancuso, A.Heyne, K.Hughes, J.

(2025) Nat Commun 16: 5319-5319

  • DOI: https://doi.org/10.1038/s41467-025-60738-w
  • Primary Citation of Related Structures:  
    8R44, 8R45, 9ER4, 9F4I, 9QZT

  • PubMed Abstract: 

    Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant.


  • Organizational Affiliation

    Institute for Plant Physiology, Justus Liebig University, Giessen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytochrome A-2
A, B
359Glycine maxMutation(s): 0 
Gene Names: PHYA2GLYMA_20G090000
UniProt
Find proteins for B4YB07 (Glycine max)
Explore B4YB07 
Go to UniProtKB:  B4YB07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4YB07
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
H [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.195 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.186 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.287α = 90
b = 111.812β = 92.308
c = 68.273γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1078

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references
  • Version 1.2: 2025-07-02
    Changes: Database references