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- PDB-6x24: Structural basis of plant blue light photoreceptor -

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Basic information

Entry
Database: PDB / ID: 6x24
TitleStructural basis of plant blue light photoreceptor
ComponentsCryptochrome-2
KeywordsSIGNALING PROTEIN / Cryptochrome / Blue-light receptors / CRY2 / Photolyase / FAD / Signaling Photoreceptor
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
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsPalayam, M. / Ganapathy, J. / Guercio, M.A. / Shabek, N.
CitationJournal: Commun Biol / Year: 2021
Title: Structural insights into photoactivation of plant Cryptochrome-2.
Authors: Palayam, M. / Ganapathy, J. / Guercio, A.M. / Tal, L. / Deck, S.L. / Shabek, N.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-2
B: Cryptochrome-2
C: Cryptochrome-2
D: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,56223
Polymers229,0384
Non-polymers4,52419
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20980 Å2
ΔGint-93 kcal/mol
Surface area73460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.362, 208.362, 81.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Cryptochrome-2 / Blue light photoreceptor / Atcry2 / Protein PHR homolog 1 / AtPHH1 / Protein SUPPRESSOR OF elf3 20


Mass: 57259.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CRY2, PHH1, SEL20, At1g04400, F19P19.14 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q96524
#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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.5M Sodium Nitrate, 0.1M BIS-TRIS propane pH=7.0, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50.05 Å / Num. obs: 61839 / % possible obs: 99.34 % / Redundancy: 1.54 % / Rrim(I) all: 0.078 / Net I/σ(I): 14.8
Reflection shellResolution: 3.25→3.36 Å / Num. unique obs: 6050 / CC star: 0.744 / Rrim(I) all: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U3C

1u3c


Resolution: 3.25→50.05 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 36.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3285 1992 3.22 %
Rwork0.2713 59847 -
obs0.2732 61839 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.05 Å2 / Biso mean: 53.8013 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: final / Resolution: 3.25→50.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15279 0 302 30 15611
Biso mean--44.87 19.98 -
Num. residues----1879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.330.37821360.334151428797
3.33-3.420.39081450.32254334447999
3.42-3.520.41131450.307142674412100
3.53-3.640.35731360.296342844420100
3.64-3.770.35751440.293242954439100
3.77-3.920.36211420.288343224464100
3.92-4.10.37511470.272342824429100
4.1-4.310.35351490.251543124461100
4.31-4.580.29251400.246442504390100
4.58-4.940.26041480.237942984446100
4.94-5.430.31741450.25343114456100
5.43-6.220.30171360.272842644400100
6.22-7.830.27891520.27524234438699
7.83-50.050.27441270.24414243437098

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