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- EMDB-30128: Cryo-EM structure of Arabidopsis CRY under blue light-mediated ac... -

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Basic information

Entry
Database: EMDB / ID: EMD-30128
TitleCryo-EM structure of Arabidopsis CRY under blue light-mediated activation
Map data
Sample
  • Complex: blue-light activated Arabidopsis thaliana CRY2 tetramer
    • Protein or peptide: Cryptochrome-2
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
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 / blue light signaling pathway ...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 / blue light signaling pathway / regulation of flower development / positive regulation of flower development / 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 / metal ion binding / nucleus / 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 thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMa L / Guan ZY / Yin P
CitationJournal: Nat Plants / Year: 2020
Title: Structural insights into the photoactivation of Arabidopsis CRY2.
Authors: Ling Ma / Zeyuan Guan / Qiang Wang / Xuhui Yan / Jing Wang / Zhizheng Wang / Jianbo Cao / Delin Zhang / Xin Gong / Ping Yin /
Abstract: The blue-light receptor cryptochrome (CRY) in plants undergoes oligomerization to transduce blue-light signals after irradiation, but the corresponding molecular mechanism remains poorly understood. ...The blue-light receptor cryptochrome (CRY) in plants undergoes oligomerization to transduce blue-light signals after irradiation, but the corresponding molecular mechanism remains poorly understood. Here, we report the cryogenic electron microscopy structure of a blue-light-activated CRY2 tetramer at a resolution of 3.1 Å, which shows how the CRY2 tetramer assembles. Our study provides insights into blue-light-mediated activation of CRY2 and a theoretical basis for developing regulators of CRYs for optogenetic manipulation.
History
DepositionMar 18, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateAug 4, 2021-
Current statusAug 4, 2021Processing site: PDBj / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.03
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  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6m79
  • Surface level: 0.03
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30128.png

Downloads & links

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Map

FileDownload / File: emd_30128.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.03
Minimum - Maximum-0.12942281 - 0.26605147
Average (Standard dev.)-3.0297784e-05 (±0.0070872717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z266.400266.400266.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1290.266-0.000

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Supplemental data

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Half map: #2

Fileemd_30128_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_30128_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 : blue-light activated Arabidopsis thaliana CRY2 tetramer

EntireName: blue-light activated Arabidopsis thaliana CRY2 tetramer
Components
  • Complex: blue-light activated Arabidopsis thaliana CRY2 tetramer
    • Protein or peptide: Cryptochrome-2
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide

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Supramolecule #1: blue-light activated Arabidopsis thaliana CRY2 tetramer

SupramoleculeName: blue-light activated Arabidopsis thaliana CRY2 tetramer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 69.57993 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKMDKKTIVW FRRDLRIEDN PALAAAAHEG SVFPVFIWCP EEEGQFYPGR ASRWWMKQSL AHLSQSLKAL GSDLTLIQTH NTISAILDC IRVTGPTKVV FNHLYDPVSL VRDHTVKEKL VERGISVQSY NGDLLYEPWE IYCEKGKPFT SFNSYWKKCL D MSIESVML ...String:
MKMDKKTIVW FRRDLRIEDN PALAAAAHEG SVFPVFIWCP EEEGQFYPGR ASRWWMKQSL AHLSQSLKAL GSDLTLIQTH NTISAILDC IRVTGPTKVV 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 RIRVIVSSFG VKFLLLPWKW GMKYFWDTLL DADLECDILG WQYI SGSIP DGHELDRLDN PALQGAKYDP EGEYIRQWLP ELARLPTEWI HHPWDAPLTV LKASGVELGT NYAKPIVDID TAREL LAKA ISRTREAQIM IGAAPDEIVA DSFEALGANT IKEPGLCPSV SSNDQQVPSV VRYNGSKRVK PEEEEERDMK KSRGFD ERE LFSTAESSSS SSVFFVSQSC SLASEGKNLE GIQDSSDQIT TSLGKNGCK

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Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

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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 / Flavin adenine dinucleotide

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. v1.18)
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0-beta-2)
Final 3D classificationSoftware - Name: RELION (ver. 3.0-beta-2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0-beta-2)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 209604

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