9ITF | pdb_00009itf

Cryo-EM structure of full-length phyB(Y276H)-PIF6beta complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytochrome BA [auth C],
B [auth A]
1,226Arabidopsis thalianaMutation(s): 1 
Gene Names: PHYBHY3OOP1At2g18790MSF3.17
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor PIF6C [auth B]241Arabidopsis thalianaMutation(s): 0 
Gene Names: PIF6BHLH132EN111PIL2At3g62090T17J13.50
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 (Subject of Investigation/LOI)
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: 2.90 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: 2025-07-23
    Changes: Data collection