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- EMDB-32929: Cryo-EM Structure of Arabidopsis CRY2 tetramer in complex with CI... -

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Basic information

Entry
Database: EMDB / ID: EMD-32929
TitleCryo-EM Structure of Arabidopsis CRY2 tetramer in complex with CIB1 fragment
Map data
Sample
  • Complex: Arabidosis CRY2 tetramer in complex with CIB1 fragment
    • Protein or peptide: Cryptochrome-2
    • Protein or peptide: CIB1 fragment
  • 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 / 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 / blue light signaling pathway / regulation of photoperiodism, flowering ...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 / blue light signaling pathway / regulation of photoperiodism, flowering / positive regulation of flower development / regulation of flower development / phototropism / stomatal movement / response to blue light / deoxyribodipyrimidine photo-lyase activity / blue light photoreceptor activity / response to water deprivation / plant-type vacuole / entrainment of circadian clock by photoperiod / response to light stimulus / FAD binding / circadian regulation of gene expression / 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 / DNA binding / 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) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 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_32929.png

Downloads & links

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Map

FileDownload / File: emd_32929.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.74577975 - 1.4427687
Average (Standard dev.)0.0042869076 (±0.056507073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of AtCRY2(W374A)-CIB1(275) complex

Fileemd_32929_additional_1.map
AnnotationSharpened map of AtCRY2(W374A)-CIB1(275) complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32929_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32929_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 : Arabidosis CRY2 tetramer in complex with CIB1 fragment

EntireName: Arabidosis CRY2 tetramer in complex with CIB1 fragment
Components
  • Complex: Arabidosis CRY2 tetramer in complex with CIB1 fragment
    • Protein or peptide: Cryptochrome-2
    • Protein or peptide: CIB1 fragment
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Arabidosis CRY2 tetramer in complex with CIB1 fragment

SupramoleculeName: Arabidosis CRY2 tetramer in complex with CIB1 fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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 thaliana (thale cress)
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: CIB1 fragment

MacromoleculeName: CIB1 fragment / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 698.854 Da
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / 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
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180055
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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