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 9IRK | pdb_00009irk

Cryo-EM structure of PhyB(Y276H,1-908)-PIF6beta complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9IRK

This is version 1.1 of the entry. See complete history. 

Literature

Structural insight into PIF6-mediated red light signal transduction of plant phytochrome B.

Jia, H., Guan, Z., Ding, J., Wang, X., Tian, D., Zhu, Y., Zhang, D., Liu, Z., Ma, L., Yin, P.

(2025) Cell Discov 11: 51-51

  • DOI: https://doi.org/10.1038/s41421-025-00802-3
  • Primary Citation Related Structures: 
    9IRK, 9ITF, 9JLB

  • PubMed Abstract: 

    The red/far-red light receptor phytochrome B (phyB) plays essential roles in regulating various plant development processes. PhyB exists in two distinct photoreversible forms: the inactive Pr form and the active Pfr form. phyB-Pfr binds phytochrome-interacting factors (PIFs) to transduce red light signals. Here, we determined the cryo-electron microscopy (cryo-EM) structures of the photoactivated phyB-Pfr‒PIF6 complex, the constitutively active mutant phyB Y276H ‒PIF6 complex, and the truncated phyBN Y276H ‒PIF6 complex. In these structures, two parallel phyB-Pfr molecules interact with one PIF6 molecule. Red light-triggered rotation of the PΦB D-ring leads to the conversion of hairpin loops into α helices and the "head-to-head" reassembly of phyB-Pfr N-terminal photosensory modules. The interaction between phyB-Pfr and PIF6 influences the dimerization and transcriptional activation activity of PIF6, and PIF6 stabilizes the N-terminal extension of phyB-Pfr and increases the Pr→Pfr photoconversion efficiency of phyB. Our findings reveal the molecular mechanisms underlying Pr→Pfr photoconversion and PIF6-mediated red light signal transduction of phyB.


  • Organizational Affiliation: 
    • National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, Hubei, China.

Macromolecule Content 

  • Total Structure Weight: 220.09 kDa 
  • Atom Count: 8,277 
  • Modeled Residue Count: 1,052 
  • Deposited Residue Count: 1,995 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phytochrome BA [auth C],
B [auth A]
907Arabidopsis thalianaMutation(s): 1 
Gene Names: PHYB, HY3, OOP1, At2g18790, MSF3.17
UniProt
Find proteins for P14713 (Arabidopsis thaliana)
Explore P14713 
Go to UniProtKB:  P14713
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14713
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription factor PIF6C [auth B]181Arabidopsis thalianaMutation(s): 0 
Gene Names: PIF6, BHLH132, EN111, PIL2, At3g62090, T17J13.50
UniProt
Find proteins for Q8L5W7 (Arabidopsis thaliana)
Explore Q8L5W7 
Go to UniProtKB:  Q8L5W7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L5W7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O6E

Query on O6E



Download:Ideal Coordinates CCD File
D [auth C],
E [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: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection