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- PDB-7rzw: CryoEM structure of Arabidopsis thaliana phytochrome B -

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Basic information

Entry
Database: PDB / ID: 7rzw
TitleCryoEM structure of Arabidopsis thaliana phytochrome B
ComponentsPhytochrome B
KeywordsGENE REGULATION / phytochrome / asymmetric dimer
Function / homology
Function and homology information


abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / transpiration / far-red light photoreceptor activity / red light signaling pathway / regulation of defense response / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system ...abscisic acid metabolic process / response to low fluence red light stimulus / red light photoreceptor activity / protein-phytochromobilin linkage / transpiration / far-red light photoreceptor activity / red light signaling pathway / regulation of defense response / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / red or far-red light photoreceptor activity / stomatal complex development / regulation of photoperiodism, flowering / gravitropism / regulation of seed germination / jasmonic acid mediated signaling pathway / response to far red light / phototropism / photomorphogenesis / detection of visible light / entrainment of circadian clock / response to temperature stimulus / phosphorelay sensor kinase activity / photosynthesis / response to cold / promoter-specific chromatin binding / chromatin organization / sequence-specific DNA binding / nuclear body / nuclear speck / negative regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
Phytochrome A/B/C/D/E-like, histidine-kinase-related domain / Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region ...Phytochrome A/B/C/D/E-like, histidine-kinase-related domain / Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-O6E / Phytochrome B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, H. / Burgie, E.S. / Vierstra, R.D. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: Nature / Year: 2022
Title: Plant phytochrome B is an asymmetric dimer with unique signalling potential.
Authors: Hua Li / E Sethe Burgie / Zira T K Gannam / Huilin Li / Richard D Vierstra /
Abstract: Many aspects of plant photoperception are mediated by the phytochrome (Phy) family of bilin-containing photoreceptors that reversibly interconvert between inactive Pr and active Pfr conformers. ...Many aspects of plant photoperception are mediated by the phytochrome (Phy) family of bilin-containing photoreceptors that reversibly interconvert between inactive Pr and active Pfr conformers. Despite extensive biochemical studies, full understanding of plant Phy signalling has remained unclear due to the absence of relevant 3D models. Here we report a cryo-electron microscopy structure of Arabidopsis PhyB in the Pr state that reveals a topologically complex dimeric organization that is substantially distinct from its prokaryotic relatives. Instead of an anticipated parallel architecture, the C-terminal histidine-kinase-related domains (HKRDs) associate head-to-head, whereas the N-terminal photosensory regions associate head-to-tail to form a parallelogram-shaped platform with near two-fold symmetry. The platform is internally linked by the second of two internal Per/Arnt/Sim domains that binds to the photosensory module of the opposing protomer and a preceding 'modulator' loop that assembles tightly with the photosensory module of its own protomer. Both connections accelerate the thermal reversion of Pfr back to Pr, consistent with an inverse relationship between dimer assembly and Pfr stability. Lopsided contacts between the HKRDs and the platform create profound asymmetry to PhyB that might imbue distinct signalling potentials to the protomers. We propose that this unique structural dynamism creates an extensive photostate-sensitive surface for conformation-dependent interactions between plant Phy photoreceptors and their signalling partners.
History
DepositionAug 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytochrome B
B: Phytochrome B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,1194
Polymers258,9462
Non-polymers1,1732
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Phytochrome B / Protein LONG HYPOCOTYL 3 / Protein OUT OF PHASE 1


Mass: 129473.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHYB, HY3, OOP1, At2g18790, MSF3.17 / Production host: Escherichia coli (E. coli) / References: UniProt: P14713
#2: Chemical ChemComp-O6E / 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
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: Phytochrome / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
175 mMpotassium chlorideKCl1
220 mMHEPESC9H20N2O4S1
310 mM2-MercaptoethanolC2H6OS1
40.01 mMEDTAEthylenediaminetetraacetic acidC10H16N2O81
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 279 K

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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: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80.15 K / Temperature (min): 80.15 K / Residual tilt: 0.05 mradians
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 54.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6153
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.18_3861: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION2CTF correction
9RELION2initial Euler assignment
11RELION2classification
12RELION33D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 902965
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154901 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00513880
ELECTRON MICROSCOPYf_angle_d1.03718763
ELECTRON MICROSCOPYf_dihedral_angle_d23.3795193
ELECTRON MICROSCOPYf_chiral_restr0.0562101
ELECTRON MICROSCOPYf_plane_restr0.0082407

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