9LH4 | pdb_00009lh4

Crystal structure of the cyclophilin 37 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb9LH4/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-11 Released: 2025-12-24 
• Deposition Author(s): Dong, S., Qin, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of cyclophilin 37 from Arabidopsis thaliana.

Han, X., Jiang, J., Lu, Z., Bai, J., Qin, X., Dong, S.

(2025) Acta Crystallogr F Struct Biol Commun 81: 171-176

• PubMed: 40091855 
• DOI: https://doi.org/10.1107/S2053230X25001979
• Primary Citation of Related Structures:  
  9LH4


• PubMed Abstract: 
  

  Photosynthesis is the largest-scale energy and material conversion process on Earth. The cytchrome (Cyt) b ₆ f complex plays a crucial role in photosynthesis. Under high-light conditions, cyclophilin 37 (CYP37) in Arabidopsis thaliana (AtCYP37) can interact with the PetA subunit of Cyt b ₆ f, thereby helping plants initiate photoprotection. Here, we purified, crystallized and determined a 1.95 Å resolution structure of AtCYP37. Overall, AtCYP37 consists of an N-terminal domain dominated by α-helices and a C-terminal domain mainly composed of β-strands and random coils. The structure shows significant similarity to those of Anabaena sp. CYPA and A. thaliana CYP38. Understanding the structure of AtCYP37 is significant as it may help to decipher how plants regulate photosynthesis and protect against high light damage, contributing to a broader understanding of plant photobiology and potentially guiding future research in improving plant stress tolerance.

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Organizational Affiliation: 
• School of Biological Science and Technology, University of Jinan, Jinan, Shandong 250022, People's Republic of China.
Food and Pharmacy College, Xuchang University, Xuchang, Henan 461000, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.44 kDa 
• Atom Count: 2,743 
• Modeled Residue Count: 333 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase CYP37, chloroplastic	A	386	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CYP37, At3g15520, MJK13.18 EC: 5.2.1.8
UniProt
Find proteins for P82869 (Arabidopsis thaliana) Explore P82869  Go to UniProtKB:  P82869

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.095	α = 90
b = 71.095	β = 90
c = 137.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Dong, S., Qin, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200206; 32270260; 32070267

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release