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Yorodumi- EMDB-32929: Cryo-EM Structure of Arabidopsis CRY2 tetramer in complex with CI... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32929 | |||||||||
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Title | Cryo-EM Structure of Arabidopsis CRY2 tetramer in complex with CIB1 fragment | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cryptochrome / Photoreceptor / Photosignaling / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / response to absence of light / circadian regulation of calcium ion oscillation / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / regulation of leaf morphogenesis / regulation of photoperiodism, flowering / positive regulation of flower development ...flavin adenine dinucleotide metabolic process / long-day photoperiodism, flowering / response to absence of light / circadian regulation of calcium ion oscillation / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / regulation of leaf morphogenesis / 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 / circadian rhythm / PML body / positive regulation of reactive oxygen species metabolic process / chromatin organization / defense response to virus / chromatin remodeling / nuclear body / protein homodimerization activity / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis (plant) / Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
Authors | Hao YH / Zhang X | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32929.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-32929-v30.xml emd-32929.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_32929.png | 168.9 KB | ||
Filedesc metadata | emd-32929.cif.gz | 5.5 KB | ||
Others | emd_32929_additional_1.map.gz emd_32929_half_map_1.map.gz emd_32929_half_map_2.map.gz | 27.3 MB 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32929 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32929 | HTTPS FTP |
-Validation report
Summary document | emd_32929_validation.pdf.gz | 929.4 KB | Display | EMDB validaton report |
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Full document | emd_32929_full_validation.pdf.gz | 929 KB | Display | |
Data in XML | emd_32929_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_32929_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32929 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32929 | HTTPS FTP |
-Related structure data
Related structure data | 7x0yMC 7x0xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32929.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sharpened map of AtCRY2(W374A)-CIB1(275) complex
File | emd_32929_additional_1.map | ||||||||||||
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Annotation | Sharpened map of AtCRY2(W374A)-CIB1(275) complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32929_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32929_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Arabidosis CRY2 tetramer in complex with CIB1 fragment
Entire | Name: Arabidosis CRY2 tetramer in complex with CIB1 fragment |
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Components |
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-Supramolecule #1: Arabidosis CRY2 tetramer in complex with CIB1 fragment
Supramolecule | Name: Arabidosis CRY2 tetramer in complex with CIB1 fragment type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Arabidopsis (plant) |
-Macromolecule #1: Cryptochrome-2
Macromolecule | Name: Cryptochrome-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 69.425789 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKMDKKTIVW FRRDLRIEDN PALAAAAHEG SVFPVFIWCP EEEGQFYPGR ASRWWMKQSL AHLSQSLKAL GSDLTLIKTH NTISAILDC IRVTGATKVV FNHLYDPVSL VRDHTVKEKL VERGISVQSY NGDLLYEPWE IYCEKGKPFT SFNSYWKKCL D MSIESVML ...String: MKMDKKTIVW FRRDLRIEDN PALAAAAHEG SVFPVFIWCP EEEGQFYPGR ASRWWMKQSL AHLSQSLKAL GSDLTLIKTH NTISAILDC IRVTGATKVV FNHLYDPVSL VRDHTVKEKL VERGISVQSY NGDLLYEPWE IYCEKGKPFT SFNSYWKKCL D MSIESVML PPPWRLMPIT AAAEAIWACS IEELGLENEA EKPSNALLTR AWSPGWSNAD KLLNEFIEKQ LIDYAKNSKK VV GNSTSLL SPYLHFGEIS VRHVFQCARM KQIIWARDKN SEGEESADLF LRGIGLREYS RYICFNFPFT HEQSLLSHLR FFP WDADVD KFKAWRQGRT GYPLVDAGMR ELWATGWMHN RIRVIVSSFA VKFLLLPAKW GMKYFWDTLL DADLECDILG WQYI SGSIP DGHELDRLDN PALQGAKYDP EGEYIRQWLP ELARLPTEWI HHPWDAPLTV LKASGVELGT NYAKPIVDID TAREL LAKA ISRTREAQIM IGAAPDEIVA DSFEALGANT IKEPGLCPSV SSNDQQVPSA VRYNGSKRVK PEEEEERDMK KSRGFD ERE LFSTAESSSS SSVFFVSQSC SLASEGKNLE GIQDSSDQIT TSLGKNGCK UniProtKB: Cryptochrome-2 |
-Macromolecule #2: CIB1 fragment
Macromolecule | Name: CIB1 fragment / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 698.854 Da |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180055 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |