6M79

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.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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 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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41477-020-00800-1
Primary Citation of 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.

Organizational Affiliation

National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96524
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]