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- EMDB-24780: CryoEM map of Arabidopsis thaliana phytochrome B -

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Basic information

Entry
Database: EMDB / ID: EMD-24780
TitleCryoEM map of Arabidopsis thaliana phytochrome B
Map data
Sample
  • Complex: Phytochrome
    • Protein or peptide: Phytochrome B
  • Ligand: 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
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
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi H / Burgie ES / Vierstra RD
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateApr 20, 2022-
Current statusApr 20, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24780.png

Downloads & links

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Map

FileDownload / File: emd_24780.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.029 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.09693297 - 0.16743304
Average (Standard dev.)0.0002540493 (±0.0036864153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.424 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_24780_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24780_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phytochrome

EntireName: Phytochrome
Components
  • Complex: Phytochrome
    • Protein or peptide: Phytochrome B
  • Ligand: 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

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Supramolecule #1: Phytochrome

SupramoleculeName: Phytochrome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Phytochrome B

MacromoleculeName: Phytochrome B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 129.473047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...

MacromoleculeName: 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
Molecular weightTheoretical: 586.678 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
75.0 mMKClpotassium chloride
20.0 mMC9H20N2O4SHEPES
10.0 mMC2H6OS2-Mercaptoethanol
0.01 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.15 K / Max: 80.15 K
Alignment procedureComa free - Residual tilt: 0.05 mrad
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 902965
CTF correctionSoftware - Name: RELION (ver. 2)
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 154901
FSC plot (resolution estimation)

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