8F5Z

Composite map of CryoEM structure of Arabidopsis thaliana phytochrome A

  • Classification: GENE REGULATION
  • Organism(s): Arabidopsis thaliana
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-11-15 Released: 2023-06-28 
  • Deposition Author(s): Li, H., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms.

Burgie, E.S.Li, H.Gannam, Z.T.K.McLoughlin, K.E.Vierstra, R.D.Li, H.

(2023) Nat Plants 9: 1116-1129

  • DOI: https://doi.org/10.1038/s41477-023-01435-8
  • Primary Citation of Related Structures:  
    8F5Z

  • PubMed Abstract: 

    Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception.


  • Organizational Affiliation

    Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytochrome AA [auth B],
B [auth A]
1,123Arabidopsis thalianaMutation(s): 0 
Gene Names: PHYAFHY2FRE1HY8At1g09570F14J9.23
UniProt
Find proteins for P14712 (Arabidopsis thaliana)
Explore P14712 
Go to UniProtKB:  P14712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14712
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O6E (Subject of Investigation/LOI)
Query on O6E

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid
C33 H38 N4 O6
SRFSSETUPHUBBC-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-06-28 
  • Deposition Author(s): Li, H., Li, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131754

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references