8IFF | pdb_00008iff

Cryo-EM structure of Arabidopsis phytochrome A.

• PDB DOI: https://doi.org/10.2210/pdb8IFF/pdb
• EM Map EMD-35415: EMDB EMDataResource

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


• Deposited: 2023-02-17 Released: 2023-08-02 
• Deposition Author(s): Ma, L., Zhou, C., Wang, J., Guan, Z., Yin, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Plant phytochrome A in the Pr state assembles as an asymmetric dimer.

Wang, J., Zhou, C., Guan, Z., Wang, Q., Zhao, J., Wang, L., Zhang, L., Zhang, D., Deng, X.W., Ma, L., Yin, P.

(2023) Cell Res 33: 802-805

• PubMed: 37402899 
• DOI: https://doi.org/10.1038/s41422-023-00847-7
• Primary Citation Related Structures: 
  8IFF

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China.
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China. [e-mail].
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 250.48 kDa 
• Atom Count: 13,698 
• Modeled Residue Count: 1,736 
• Deposited Residue Count: 2,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome A	A, B	1,122	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PHYA, FHY2, FRE1, HY8, At1g09570, F14J9.23
UniProt
Find proteins for P14712 (Arabidopsis thaliana) Explore P14712  Go to UniProtKB:  P14712

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O6E	C [auth A], D [auth B]	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: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Ma, L., Zhou, C., Wang, J., Guan, Z., Yin, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references
• Version 1.2: 2025-07-23
  Changes: Data collection, Structure summary