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- PDB-8iff: Cryo-EM structure of Arabidopsis phytochrome A. -

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Basic information

Entry
Database: PDB / ID: 8iff
TitleCryo-EM structure of Arabidopsis phytochrome A.
ComponentsPhytochrome A
KeywordsGENE REGULATION / phytochrome / Pr state
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 / negative regulation of translation / nuclear body / protein kinase activity / 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
Chem-O6E / Phytochrome A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMa, L. / Zhou, C. / Wang, J. / Guan, Z. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2023
Title: Plant phytochrome A in the Pr state assembles as an asymmetric dimer.
Authors: Jiao Wang / Chen Zhou / Zeyuan Guan / Qiang Wang / Jun Zhao / Lixia Wang / Liuqing Zhang / Delin Zhang / Xing Wang Deng / Ling Ma / Ping Yin /
History
DepositionFeb 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytochrome A
B: Phytochrome A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,4794
Polymers249,3062
Non-polymers1,1732
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Phytochrome A / Protein ELONGATED HYPOCOTYL 8 / Protein FAR RED ELONGATED 1 / Protein FAR RED ELONGATED HYPOCOTYL 2


Mass: 124652.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Author stated the additional map was 3.4 angstrom with improved HKRD domain.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHYA, FHY2, FRE1, HY8, At1g09570, F14J9.23 / Production host: Arabidopsis (plant) / References: UniProt: P14712
#2: Chemical 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


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Phytochrome A / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Arabidopsis (plant)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 498817 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413952
ELECTRON MICROSCOPYf_angle_d0.83818839
ELECTRON MICROSCOPYf_dihedral_angle_d12.421892
ELECTRON MICROSCOPYf_chiral_restr0.0422147
ELECTRON MICROSCOPYf_plane_restr0.0042400

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