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Yorodumi- PDB-7x0y: Cryo-EM Structure of Arabidopsis CRY2 tetramer in complex with CI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x0y | ||||||
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Title | Cryo-EM Structure of Arabidopsis CRY2 tetramer in complex with CIB1 fragment | ||||||
Components |
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Keywords | PLANT PROTEIN / Cryptochrome / Photoreceptor / Photosignaling | ||||||
Function / homology | Function and homology information flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / response to absence of light / response to strigolactone / regulation of meristem growth / regulation of leaf morphogenesis / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / regulation of photoperiodism, flowering / positive regulation of flower development ...flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / response to absence of light / response to strigolactone / regulation of meristem growth / regulation of leaf morphogenesis / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / regulation of photoperiodism, flowering / positive regulation of flower development / regulation of flower development / blue light signaling pathway / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / response to water deprivation / plant-type vacuole / response to light stimulus / FAD binding / regulation of circadian rhythm / PML body / 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 / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å | ||||||
Authors | Hao, Y.H. / Zhang, X. / Zhang, P. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x0y.cif.gz | 457.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x0y.ent.gz | 353.6 KB | Display | PDB format |
PDBx/mmJSON format | 7x0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x0y_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7x0y_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7x0y_validation.xml.gz | 70.1 KB | Display | |
Data in CIF | 7x0y_validation.cif.gz | 100 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0y ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0y | HTTPS FTP |
-Related structure data
Related structure data | 32929MC 7x0xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 69425.789 Da / Num. of mol.: 4 / Mutation: W374A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRY2, PHH1, SEL20, At1g04400, F19P19.14 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96524 #2: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Spodoptera frugiperda (fall armyworm) #3: Chemical | ChemComp-FAD / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Arabidosis CRY2 tetramer in complex with CIB1 fragment Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis (plant) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180055 / Symmetry type: POINT |