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- EMDB-32928: Cryo-EM Structure of Arabidopsis CRY2 in active conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-32928
TitleCryo-EM Structure of Arabidopsis CRY2 in active conformation
Map data
Sample
  • Complex: Tetrameric complex of Arabidosis CRY2
    • Protein or peptide: Cryptochrome-2
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsCryptochrome / Photoreceptor / Photosignaling / PLANT PROTEIN
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 / positive regulation of flower development / regulation of photoperiodism, flowering ...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 / positive regulation of flower development / regulation of photoperiodism, flowering / 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
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
Biological speciesArabidopsis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsHao YH / Zhang X
Funding support China, 1 items
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, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32928.png

Downloads & links

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Map

FileDownload / File: emd_32928.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.103038 - 7.448558
Average (Standard dev.)-0.0005001755 (±0.18644334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of AtCRY2(W374A)

Fileemd_32928_additional_1.map
AnnotationSharpened map of AtCRY2(W374A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32928_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32928_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric complex of Arabidosis CRY2

EntireName: Tetrameric complex of Arabidosis CRY2
Components
  • Complex: Tetrameric complex of Arabidosis CRY2
    • Protein or peptide: Cryptochrome-2
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Tetrameric complex of Arabidosis CRY2

SupramoleculeName: Tetrameric complex of Arabidosis CRY2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis (plant)

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Macromolecule #1: Cryptochrome-2

MacromoleculeName: Cryptochrome-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 69.425789 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244515
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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