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- EMDB-30022: Structure of cryptochrome in active conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-30022
TitleStructure of cryptochrome in active conformation
Map data
Sample
  • Complex: Tetrameric complex of ZmCRY1c
    • Protein or peptide: Cryptochrome2
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase activity / blue light photoreceptor activity / nucleobase-containing compound metabolic process / response to stress / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm
Similarity search - Function
Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / 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 C-terminal / Blue/Ultraviolet sensing protein C terminal / 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 speciesZea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShao K / Zhang X / Zhang P
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: The oligomeric structures of plant cryptochromes.
Authors: Kai Shao / Xue Zhang / Xu Li / Yahui Hao / Xiaowei Huang / Miaolian Ma / Minhua Zhang / Fang Yu / Hongtao Liu / Peng Zhang /
Abstract: Cryptochromes (CRYs) are a group of evolutionarily conserved flavoproteins found in many organisms. In plants, the well-studied CRY photoreceptor, activated by blue light, plays essential roles in ...Cryptochromes (CRYs) are a group of evolutionarily conserved flavoproteins found in many organisms. In plants, the well-studied CRY photoreceptor, activated by blue light, plays essential roles in plant growth and development. However, the mechanism of activation remains largely unknown. Here, we determined the oligomeric structures of the blue-light-perceiving PHR domain of Zea mays CRY1 and an Arabidopsis CRY2 constitutively active mutant. The structures form dimers and tetramers whose functional importance is examined in vitro and in vivo with Arabidopsis CRY2. Structure-based analysis suggests that blue light may be perceived by CRY to cause conformational changes, whose precise nature remains to be determined, leading to oligomerization that is essential for downstream signaling. This photoactivation mechanism may be widely used by plant CRYs. Our study reveals a molecular mechanism of plant CRY activation and also paves the way for design of CRY as a more efficient optical switch.
History
DepositionFeb 18, 2020-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6lz3
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30022.png

Downloads & links

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Map

FileDownload / File: emd_30022.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.)
1.06 Å/pix.
x 240 pix.
= 254.64 Å		1.06 Å/pix.
x 240 pix.
= 254.64 Å		1.06 Å/pix.
x 240 pix.
= 254.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.05
Minimum - Maximum-0.14682937 - 0.28867164
Average (Standard dev.)0.0006474543 (±0.008206731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.640254.640254.640
α/β/γ90.00090.00090.000
start NX/NY/NZ107107101
NX/NY/NZ267267267
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1470.2890.001

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Supplemental data

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Half map: #1

Fileemd_30022_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_30022_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 ZmCRY1c

EntireName: Tetrameric complex of ZmCRY1c
Components
  • Complex: Tetrameric complex of ZmCRY1c
    • Protein or peptide: Cryptochrome2
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Tetrameric complex of ZmCRY1c

SupramoleculeName: Tetrameric complex of ZmCRY1c / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Zea mays (maize)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Cryptochrome2

MacromoleculeName: Cryptochrome2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 77.609125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRIVVWFRRD LRVEDNPALA AAARAGGEVV PAYVWSPEEE GPYYPGRVSR WWISQSLNHL DASLRRLGAG KLVTRRSADA AVALLQLVR DTGATHVYFN HLYDPISLVR DRRLKEMLAA EGIVVQSFNS DLLYEPWEVV DDEGQPFTMF DPFWNRCLSM P YDPPAPLL ...String:
MRIVVWFRRD LRVEDNPALA AAARAGGEVV PAYVWSPEEE GPYYPGRVSR WWISQSLNHL DASLRRLGAG KLVTRRSADA AVALLQLVR DTGATHVYFN HLYDPISLVR DRRLKEMLAA EGIVVQSFNS DLLYEPWEVV DDEGQPFTMF DPFWNRCLSM P YDPPAPLL PPKRINSGDL SMCPSEDLIF EDESERGSNA LLARAWTPGW QNADKALTAF LNGPLADYSV NRKKADSAST SL LSPHLHF GELSVRKVFH LVRMKQLVWS NEGNHAAEES CTLFLRSIGL REYSRYLSFN HPSSHERPLL AHLRFFPWVV DES YFKIWR QGRTGYPLVD AGMRELWATG WLHDRIRVVV ASFFVKVLQL PARWGMKYFW DTLLDADLES DALGWQYITG SLPD GRELD RIDNPQFEGY KFDPHGEYVR RWIPELARLP TEWIHHPWDA PVSVLQAAGI ELGSNYPLPI VELDAAKGRL QAALS EMWQ LEAASRATMN NGTEEGLGDS SEVLFPQELQ MEVDRQPAPA EAAANVHVHV PMPARRRGDQ MVPTMTTSSL NRAGTE VSA DLVVANSEEE DTRAQVPFHA HLHLHPRAEA PPAARRTNNG ARQHDVFQQR RNHRRDALLA PSASEASSSW TGREGAV VP VWSPPAASGH SDAFAADEAD VSSRSYLGRH PQSHRLMNWS QLSQSS

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108059
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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