6M79 | pdb_00006m79

Cryo-EM structure of Arabidopsis CRY under blue light-mediated activation

• PDB DOI: https://doi.org/10.2210/pdb6M79/pdb
• EM Map EMD-30128: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-03-18 Released: 2020-10-14 
• Deposition Author(s): Ma, L., Guan, Z.Y., Yin, P.

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Experimental Data Snapshot

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

Literature

Structural insights into the photoactivation of Arabidopsis CRY2.

Ma, L., Guan, Z., Wang, Q., Yan, X., Wang, J., Wang, Z., Cao, J., Zhang, D., Gong, X., Yin, P.

(2020) Nat Plants 6: 1432-1438

• PubMed: 33199893 
• DOI: https://doi.org/10.1038/s41477-020-00800-1
• Primary Citation Related Structures: 
  6M79


• PubMed Abstract: 
  

  The blue-light receptor cryptochrome (CRY) in plants undergoes oligomerization to transduce blue-light signals after irradiation, but the corresponding molecular mechanism remains poorly understood. Here, we report the cryogenic electron microscopy structure of a blue-light-activated CRY2 tetramer at a resolution of 3.1 Å, which shows how the CRY2 tetramer assembles. Our study provides insights into blue-light-mediated activation of CRY2 and a theoretical basis for developing regulators of CRYs for optogenetic manipulation.

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.
Kobilka Institute of Innovative Drug Discovery, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
School of Life Sciences, University of Science and Technology of China, Hefei, China.
Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, P. R. China.
Public Laboratory of Electron Microscopy, Huazhong Agricultural University, Wuhan, China.
Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 282.85 kDa 
• Atom Count: 15,324 
• Modeled Residue Count: 1,842 
• Deposited Residue Count: 2,448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome-2	A, B, C, D	612	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CRY2, PHH1, SEL20, At1g04400, F19P19.14
UniProt
Find proteins for Q96524 (Arabidopsis thaliana) Explore Q96524  Go to UniProtKB:  Q96524

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
AMP (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-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
RECONSTRUCTION	RELION	3.0-beta-2
MODEL REFINEMENT	PHENIX	1.16

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Ma, L., Guan, Z.Y., Yin, P.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2021-08-04
  Changes: Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2025-09-17
  Changes: Advisory, Data collection, Derived calculations