+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24780 | |||||||||
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Title | CryoEM map of Arabidopsis thaliana phytochrome B | |||||||||
Map data | ||||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Li H / Burgie ES / Vierstra RD | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24780.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-24780-v30.xml emd-24780.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24780_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_24780.png | 105.8 KB | ||
Others | emd_24780_half_map_1.map.gz emd_24780_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24780 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24780 | HTTPS FTP |
-Validation report
Summary document | emd_24780_validation.pdf.gz | 635.6 KB | Display | EMDB validaton report |
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Full document | emd_24780_full_validation.pdf.gz | 635.1 KB | Display | |
Data in XML | emd_24780_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_24780_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24780 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24780 | HTTPS FTP |
-Related structure data
Related structure data | 7rzwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24780.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.029 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_24780_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_24780_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Phytochrome
Entire | Name: Phytochrome |
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Components |
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-Supramolecule #1: Phytochrome
Supramolecule | Name: Phytochrome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Phytochrome B
Macromolecule | Name: Phytochrome B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 129.473047 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN TESMSKAIQQ YTVDARLHAV FEQSGESGKS FDYSQSLKT TTYGSSVPEQ QITAYLSRIQ RGGYIQPFGC MIAVDESSFR IIGYSENARE MLGIMPQSVP TLEKPEILAM G TDVRSLFT ...String: MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN TESMSKAIQQ YTVDARLHAV FEQSGESGKS FDYSQSLKT TTYGSSVPEQ QITAYLSRIQ RGGYIQPFGC MIAVDESSFR IIGYSENARE MLGIMPQSVP TLEKPEILAM G TDVRSLFT SSSSILLERA FVAREITLLN PVWIHSKNTG KPFYAILHRI DVGVVIDLEP ARTEDPALSI AGAVQSQKLA VR AISQLQA LPGGDIKLLC DTVVESVRDL TGYDRVMVYK FHEDEHGEVV AESKRDDLEP YIGLHYPATD IPQASRFLFK QNR VRMIVD CNATPVLVVQ DDRLTQSMCL VGSTLRAPHG CHSQYMANMG SIASLAMAVI INGNEDDGSN VASGRSSMRL WGLV VCHHT SSRCIPFPLR YACEFLMQAF GLQLNMELQL ALQMSEKRVL RTQTLLCDML LRDSPAGIVT QSPSIMDLVK CDGAA FLYH GKYYPLGVAP SEVQIKDVVE WLLANHADST GLSTDSLGDA GYPGAAALGD AVCGMAVAYI TKRDFLFWFR SHTAKE IKW GGAKHHPEDK DDGQRMHPRS SFQAFLEVVK SRSQPWETAE MDAIHSLQLI LRDSFKESEA AMNSKVVDGV VQPCRDM AG EQGIDELGAV AREMVRLIET ATVPIFAVDA GGCINGWNAK IAELTGLSVE EAMGKSLVSD LIYKENEATV NKLLSRAL R GDEEKNVEVK LKTFSPELQG KAVFVVVNAC SSKDYLNNIV GVCFVGQDVT SQKIVMDKFI NIQGDYKAIV HSPNPLIPP IFAADENTCC LEWNMAMEKL TGWSRSEVIG KMIVGEVFGS CCMLKGPDAL TKFMIVLHNA IGGQDTDKFP FPFFDRNGKF VQALLTANK RVSLEGKVIG AFCFLQIPSP ELQQALAVQR RQDTECFTKA KELAYICQVI KNPLSGMRFA NSLLEATDLN E DQKQLLET SVSCEKQISR IVGDMDLESI EDGSFVLKRE EFFLGSVINA IVSQAMFLLR DRGLQLIRDI PEEIKSIEVF GD QIRIQQL LAEFLLSIIR YAPSQEWVEI HLSQLSKQMA DGFAAIRTEF RMACPGEGLP PELVRDMFHS SRWTSPEGLG LSV CRKILK LMNGEVQYIR ESERSYFLII LELPVPRKRP LSTASGSGDM MLMMPY |
-Macromolecule #2: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...
Macromolecule | Name: 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- ...Name: 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 type: ligand / ID: 2 / Number of copies: 2 / Formula: O6E |
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Molecular weight | Theoretical: 586.678 Da |
Chemical component information | ChemComp-O6E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.8 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.15 K / Max: 80.15 K |
Alignment procedure | Coma free - Residual tilt: 0.05 mrad |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6153 / Average exposure time: 0.2 sec. / Average electron dose: 54.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |