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- EMDB-28869: Composite map of CryoEM structure of Arabidopsis thaliana phytoch... -

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Basic information

Entry
Database: EMDB / ID: EMD-28869
TitleComposite map of CryoEM structure of Arabidopsis thaliana phytochrome A
Map data
Sample
  • Complex: phytochrome A
    • Protein or peptide: Phytochrome A
  • 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
Keywordsphytochrome / asymmetric dimer / gene regulation
Function / homology
Function and homology information


response to continuous far red light stimulus by the high-irradiance response system / response to very low fluence red light stimulus / far-red light photoreceptor activity / red light signaling pathway / red or far-red light photoreceptor activity / gravitropism / response to far red light / phototropism / photomorphogenesis / detection of visible light ...response to continuous far red light stimulus by the high-irradiance response system / response to very low fluence red light stimulus / far-red light photoreceptor activity / red light signaling pathway / red or far-red light photoreceptor activity / gravitropism / response to far red light / phototropism / photomorphogenesis / detection of visible light / response to arsenic-containing substance / phosphorelay sensor kinase activity / response to cold / nuclear body / protein kinase activity / negative regulation of translation / nuclear speck / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus / cytoplasm
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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / 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: 3.2 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28869.png

Downloads & links

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Map

FileDownload / File: emd_28869.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0017233642 - 1.867665
Average (Standard dev.)0.0016008603 (±0.028677208)
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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Sample components

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Entire : phytochrome A

EntireName: phytochrome A
Components
  • Complex: phytochrome A
    • Protein or peptide: Phytochrome A
  • 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 A

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

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Macromolecule #1: Phytochrome A

MacromoleculeName: Phytochrome A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 124.70982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLA LDEKTFKVIA YSENASELLT MASHAVPSVG EHPVLGIGTD IRSLFTAPSA SALQKALGFG DVSLLNPILV H CRTSAKPF ...String:
GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLA LDEKTFKVIA YSENASELLT MASHAVPSVG EHPVLGIGTD IRSLFTAPSA SALQKALGFG DVSLLNPILV H CRTSAKPF YAIIHRVTGS IIIDFEPVKP YEVPMTAAGA LQSYKLAAKA ITRLQSLPSG SMERLCDTMV QEVFELTGYD RV MAYKFHE DDHGEVVSEV TKPGLEPYLG LHYPATDIPQ AARFLFMKNK VRMIVDCNAK HARVLQDEKL SFDLTLCGST LRA PHSCHL QYMANMDSIA SLVMAVVVNE EDGEGDAPDA TTQPQKRKRL WGLVVCHNTT PRFVPFPLRY ACEFLAQVFA IHVN KEVEL DNQMVEKNIL RTQTLLCDML MRDAPLGIVS QSPNIMDLVK CDGAALLYKD KIWKLGTTPS EFHLQEIASW LCEYH MDST GLSTDSLHDA GFPRALSLGD SVCGMAAVRI SSKDMIFWFR SHTAGEVRWG GAKHDPDDRD DARRMHPRSS FKAFLE VVK TRSLPWKDYE MDAIHSLQLI LRNAFKDSET TDVNTKVIYS KLNDLKIDGI QELEAVTSEM VRLIETATVP ILAVDSD GL VNGWNTKIAE LTGLSVDEAI GKHFLTLVED SSVEIVKRML ENALEGTEEQ NVQFEIKTHL SRADAGPISL VVNACASR D LHENVVGVCF VAHDLTGQKT VMDKFTRIEG DYKAIIQNPN PLIPPIFGTD EFGWCTEWNP AMSKLTGLKR EEVIDKMLL GEVFGTQKSC CRLKNQEAFV NLGIVLNNAV TSQDPEKVSF AFFTRGGKYV ECLLCVSKKL DREGVVTGVF CFLQLASHEL QQALHVQRL AERTAVKRLK ALAYIKRQIR NPLSGIMFTR KMIEGTELGP EQRRILQTSA LCQKQLSKIL DDSDLESIIE G CLDLEMKE FTLNEVLTAS TSQVMMKSNG KSVRITNETG EEVMSDTLYG DSIRLQQVLA DFMLMAVNFT PSGGQLTVSA SL RKDQLGR SVHLANLEIR LTHTGAGIPE FLLNQMFGTE EDVSEEGLSL MVSRKLVKLM NGDVQYLRQA GKSSFIITAE LAA ANK

UniProtKB: Phytochrome A

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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

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 / Pretreatment - Time: 30 sec.
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

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8f5z:
Composite map of CryoEM structure of Arabidopsis thaliana phytochrome A

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