6TBY

Phycocyanobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural insights into photoactivation and signalling in plant phytochromes.

Nagano, S.Guan, K.Shenkutie, S.M.Feiler, C.Weiss, M.Kraskov, A.Buhrke, D.Hildebrandt, P.Hughes, J.

(2020) Nat Plants 6: 581-588

  • DOI: https://doi.org/10.1038/s41477-020-0638-y
  • Primary Citation of Related Structures:  
    6TBY, 6TC5, 6TC7, 6TL4

  • PubMed Abstract: 

    Plant phytochromes are red/far-red photochromic photoreceptors that act as master regulators of development, controlling the expression of thousands of genes. Here, we describe the crystal structures of four plant phytochrome sensory modules, three at about 2 Å resolution or better, including the first of an A-type phytochrome. Together with extensive spectral data, these structures provide detailed insight into the structure and function of plant phytochromes. In the Pr state, the substitution of phycocyanobilin and phytochromobilin cofactors has no structural effect, nor does the amino-terminal extension play a significant functional role. Our data suggest that the chromophore propionates and especially the phytochrome-specific domain tongue act differently in plant and prokaryotic phytochromes. We find that the photoproduct in period-ARNT-single-minded (PAS)-cGMP-specific phosphodiesterase-adenylyl cyclase-FhlA (GAF) bidomains might represent a novel intermediate between MetaRc and Pfr. We also discuss the possible role of a likely nuclear localization signal specific to and conserved in the phytochrome A lineage.


  • Organizational Affiliation

    Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Gießen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PhytochromeA [auth AAA]353Sorghum bicolorMutation(s): 0 
Gene Names: PHYBSORBI_3001G394400
UniProt
Find proteins for P93527 (Sorghum bicolor)
Explore P93527 
Go to UniProtKB:  P93527
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93527
Sequence Annotations
Expand
  • 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 
B [auth AAA]PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth AAA],
G [auth AAA]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
D [auth AAA],
E [auth AAA]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.738α = 90
b = 134.738β = 90
c = 46.543γ = 120
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 FoundationGermanySFB 1078

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-05-27
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description