+Open data
-Basic information
Entry | Database: PDB / ID: 8isj | ||||||
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Title | Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr | ||||||
Components | Phytochrome A | ||||||
Keywords | PLANT PROTEIN / phytochrome A / Pr conformer / far-red light receptor | ||||||
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 | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Zhang, Y. / Ma, C. / Zhao, J. / Gao, N. / Wang, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2023 Title: Structural insights into plant phytochrome A as a highly sensitized photoreceptor. Authors: Yuxuan Zhang / Xiaoli Lin / Chengying Ma / Jun Zhao / Xiaojin Shang / Zhengdong Wang / Bin Xu / Ning Gao / Xing Wang Deng / Jizong Wang / #1: Journal: Cell Res / Year: 2023 Title: Structural insights into plant phytochrome A as a highly sensitized photoreceptor. Authors: Yuxuan Zhang / Xiaoli Lin / Chengying Ma / Jun Zhao / Xiaojin Shang / Zhengdong Wang / Bin Xu / Ning Gao / Xing Wang Deng / Jizong Wang / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8isj.cif.gz | 314.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8isj.ent.gz | 248.5 KB | Display | PDB format |
PDBx/mmJSON format | 8isj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8isj_validation.pdf.gz | 545 KB | Display | wwPDB validaton report |
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Full document | 8isj_full_validation.pdf.gz | 568 KB | Display | |
Data in XML | 8isj_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 8isj_validation.cif.gz | 52.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/8isj ftp://data.pdbj.org/pub/pdb/validation_reports/is/8isj | HTTPS FTP |
-Related structure data
Related structure data | 35692MC 8isiC 8iskC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 124409.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHYA, FHY2, FRE1, HY8, At1g09570, F14J9.23 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P14712 #2: Chemical | Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Insect cell expression vector pTIE1 (others) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 774153 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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