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- PDB-7x0x: Cryo-EM Structure of Arabidopsis CRY2 in active conformation -

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Basic information

Entry
Database: PDB / ID: 7x0x
TitleCryo-EM Structure of Arabidopsis CRY2 in active conformation
ComponentsCryptochrome-2
KeywordsPLANT PROTEIN / Cryptochrome / Photoreceptor / Photosignaling
Function / homology
Function and homology information


flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / regulation of meristem growth / response to absence of light / regulation of leaf morphogenesis / response to strigolactone / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / regulation of flower development / positive regulation of flower development ...flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / regulation of meristem growth / response to absence of light / regulation of leaf morphogenesis / response to strigolactone / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / regulation of flower development / positive regulation of flower development / regulation of photoperiodism, flowering / blue light signaling pathway / phototropism / stomatal movement / blue light photoreceptor activity / response to blue light / response to water deprivation / plant-type vacuole / response to light stimulus / FAD binding / circadian rhythm / regulation of circadian rhythm / positive regulation of reactive oxygen species metabolic process / chromatin organization / defense response to virus / nuclear body / chromatin remodeling / protein homodimerization activity / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase ...Cryptochrome, plant / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-2
Similarity search - Component
Biological speciesArabidopsis (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsHao, Y.H. / Zhang, X. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant Commun / Year: 2023
Title: Cryo-EM structure of the CRY2 and CIB1 fragment complex provides insights into CIB1-mediated photosignaling.
Authors: Yahui Hao / Xue Zhang / Yaqi Liu / Miaolian Ma / Xiaowei Huang / Hongtao Liu / Peng Zhang /
History
DepositionFeb 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Cryptochrome-2
B: Cryptochrome-2
C: Cryptochrome-2
A: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,8458
Polymers277,7034
Non-polymers3,1424
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cryptochrome-2 / Atcry2 / Blue light photoreceptor / Protein PHR homolog 1 / AtPHH1 / Protein SUPPRESSOR OF elf3 20


Mass: 69425.789 Da / Num. of mol.: 4 / Mutation: W374A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant) / Gene: CRY2, PHH1, SEL20, At1g04400, F19P19.14 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96524
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric complex of Arabidosis CRY2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis (plant)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244515 / Symmetry type: POINT

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