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- PDB-9m5u: Cryo-EM structure of Arabidopsis thaliana MET1 (aa:621-1534) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9m5u | |||||||||||||||||||||||||||
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Title | Cryo-EM structure of Arabidopsis thaliana MET1 (aa:621-1534) in complex with hemimethylated DNA analog | |||||||||||||||||||||||||||
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![]() | STRUCTURAL PROTEIN/DNA / DNA methylation / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex | |||||||||||||||||||||||||||
Function / homology | ![]() zygote asymmetric cytokinesis in embryo sac / negative regulation of flower development / DNA-mediated transformation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / methyltransferase activity / methylation / chromatin binding / DNA binding / nucleus Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||||||||||||||||||||
![]() | Kikuchi, A. / Arita, K. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Reveals Evolutionarily Conserved and Distinct Structural Features of Plant CG Maintenance Methyltransferase MET1 Authors: Kikuchi, A. / Nishiyama, A. / Chiba, Y. / Nakanishi, M. / To, K.T. / Arita, K. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 53.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 63650MC ![]() 9m5xC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 102944.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DMT1, ATHIM, DDM2, DMT01, MET1, MET2, At5g49160, K21P3.3 Production host: ![]() ![]() References: UniProt: P34881, DNA (cytosine-5-)-methyltransferase |
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#2: DNA chain | Mass: 3725.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3651.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-SAH / |
#5: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: MET1:DNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 60.725 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 864086 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 2.74 Å Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||
Refine LS restraints |
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