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- PDB-6lz3: Structure of cryptochrome in active conformation -

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Basic information

Entry
Database: PDB / ID: 6lz3
TitleStructure of cryptochrome in active conformation
ComponentsCryptochrome2
KeywordsFLAVOPROTEIN / cryptochrome / photoreceptor / photosignaling / PLANT PROTEIN
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. / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 ...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. / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome2
Similarity search - Component
Biological speciesZea mays (maize)
MethodELECTRON MICROSCOPY / single 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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Cryptochrome2
B: Cryptochrome2
C: Cryptochrome2
D: Cryptochrome2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,5798
Polymers310,4374
Non-polymers3,1424
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16140 Å2
ΔGint-52 kcal/mol
Surface area74790 Å2

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Components

#1: Protein
Cryptochrome2 / ZmCRY1c


Mass: 77609.125 Da / Num. of mol.: 4 / Mutation: W368A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100194126, ZEAMMB73_Zm00001d003477 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B8A2L5
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric complex of ZmCRY1c / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Zea mays (maize)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 49.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108059 / Symmetry type: POINT

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