8ISJ | pdb_00008isj

Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr

• PDB DOI: https://doi.org/10.2210/pdb8ISJ/pdb
• EM Map EMD-35692: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2023-03-20 Released: 2023-08-09 
• Deposition Author(s): Zhang, Y., Ma, C., Zhao, J., Gao, N., Wang, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into plant phytochrome A as a highly sensitized photoreceptor.

Zhang, Y., Lin, X., Ma, C., Zhao, J., Shang, X., Wang, Z., Xu, B., Gao, N., Deng, X.W., Wang, J.

(2023) Cell Res 33: 806-809

• PubMed: 37491602 
• DOI: https://doi.org/10.1038/s41422-023-00858-4
• Primary Citation of Related Structures:  
  8ISI, 8ISJ, 8ISK

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Organizational Affiliation: 
• National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China.
State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China.
National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China. [e-mail].
State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China. [e-mail].
Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China. [e-mail].
National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China. [e-mail].
State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 249.99 kDa 
• Atom Count: 13,533 
• Modeled Residue Count: 1,716 
• Deposited Residue Count: 2,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome A	A, B	1,120	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 (Subject of Investigation/LOI)	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: 3.00 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: 2023-08-09 
Deposition Author(s): Zhang, Y., Ma, C., Zhao, J., Gao, N., Wang, J.

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

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-23
  Changes: Data collection