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- EMDB-28870: CryoEM structure of Arabidopsis thaliana phytochrome A (consensus map) -

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Basic information

Entry
Database: EMDB / ID: EMD-28870
TitleCryoEM structure of Arabidopsis thaliana phytochrome A (consensus map)
Map data
Sample
  • Complex: phytochrome A
    • Protein or peptide: Arabidopsis thaliana phytochrome A
KeywordsPhytochrome / asymmetric dimer / gene regulation
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: Nat Plants / Year: 2023
Title: The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms.
Authors: E Sethe Burgie / Hua Li / Zira T K Gannam / Katrice E McLoughlin / Richard D Vierstra / Huilin Li /
Abstract: Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The ...Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception.
History
DepositionNov 15, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28870.png

Downloads & links

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Map

FileDownload / File: emd_28870.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.165
Minimum - Maximum-3.8095653 - 5.2621403
Average (Standard dev.)0.0020776878 (±0.09642777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28870_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28870_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 A

EntireName: phytochrome A
Components
  • Complex: phytochrome A
    • Protein or peptide: Arabidopsis thaliana phytochrome A

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Supramolecule #1: phytochrome A

SupramoleculeName: phytochrome A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 249 KDa

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Macromolecule #1: Arabidopsis thaliana phytochrome A

MacromoleculeName: Arabidopsis thaliana phytochrome A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString: GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH CRTSAKPFYA ...String:
GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH CRTSAKPFYA IIHRVTGSII IDFEPVKPYE VPMTAAGALQ SYKLAAKAIT RLQSLPSGSM ERLCDTMVQE VFELTGYDRV MAYKFHEDDH GEVVSEVTKP GLEPYLGLHY PATDIPQAAR FLFMKNKVRM IVDCNAKHAR VLQDEKLSFD LTLCGSTLRA PHSCHLQYMA NMDSIASLVM AVVVNEEDGE GDAPDATTQP QKRKRLWGLV VCHNTTPRFV PFPLRYACEF LAQVFAIHVN KEVELDNQMV EKNILRTQTL LCDMLMRDAP LGIVSQSPNI MDLVKCDGAA LLYKDKIWKL GTTPSEFHLQ EIASWLCEYH MDSTGLSTDS LHDAGFPRAL SLGDSVCGMA AVRISSKDMI FWFRSHTAGE VRWGGAKHDP DDRDDARRMH PRSSFKAFLE VVKTRSLPWK DYEMDAIHSL QLILRNAFKD SETTDVNTKV IYSKLNDLKI DGIQELEAVT SEMVRLIETA TVPILAVDSD GLVNGWNTKI AELTGLSVDE AIGKHFLTLV EDSSVEIVKR MLENALEGTE EQNVQFEIKT HLSRADAGPI SLVVNACASR DLHENVVGVC FVAHDLTGQK TVMDKFTRIE GDYKAIIQNP NPLIPPIFGT DEFGWCTEWN PAMSKLTGLK REEVIDKMLL GEVFGTQKSC CRLKNQEAFV NLGIVLNNAV TSQDPEKVSF AFFTRGGKYV ECLLCVSKKL DREGVVTGVF CFLQLASHEL QQALHVQRLA ERTAVKRLKA LAYIKRQIRN PLSGIMFTRK MIEGTELGPE QRRILQTSAL CQKQLSKILD DSDLESIIEG CLDLEMKEFT LNEVLTASTS QVMMKSNGKS VRITNETGEE VMSDTLYGDS IRLQQVLADF MLMAVNFTPS GGQLTVSASL RKDQLGRSVH LANLEIRLTH TGAGIPEFLL NQMFGTEEDV SEEGLSLMVS RKLVKLMNGD VQYLRQAGKS SFIITAELAA ANK

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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

Concentration1.0 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
75.0 mMKClpotassium chloride
20.0 mMC9H20N2O4SHEPES
10.0 mMC2H6OS2-Mercaptoethanol
0.01 mMC10H16N2O8EDTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 193.0 K / Max: 193.0 K
Alignment procedureComa free - Residual tilt: 0.05 mrad
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6390 / Average exposure time: 1.0 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3777726
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 421968
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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