+Open data
-Basic information
Entry | Database: PDB / ID: 7rzw | ||||||
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Title | CryoEM structure of Arabidopsis thaliana phytochrome B | ||||||
Components | Phytochrome B | ||||||
Keywords | GENE 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 / circadian regulation of calcium ion oscillation / regulation of defense response / 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 / circadian regulation of calcium ion oscillation / regulation of defense response / response to low fluence blue light stimulus by blue low-fluence system / red or far-red light photoreceptor activity / regulation of photoperiodism, flowering / stomatal complex development / regulation of seed germination / gravitropism / 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 | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Li, H. / Burgie, E.S. / Vierstra, R.D. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rzw.cif.gz | 311.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rzw.ent.gz | 253.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rzw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7rzw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7rzw_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 7rzw_validation.cif.gz | 89.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/7rzw ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rzw | HTTPS FTP |
-Related structure data
Related structure data | 24780MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Phytochrome / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.25 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Arabidopsis thaliana (thale cress) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 279 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: 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 recording | Average 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 scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.18_3861: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 902965 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154901 / Symmetry type: POINT | ||||||||||||||||||||||||||||
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