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- PDB-8sjd: Cryo-EM structure of the Hermes transposase bound to two right-en... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sjd | ||||||
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Title | Cryo-EM structure of the Hermes transposase bound to two right-ends of its DNA transposon. | ||||||
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![]() | RECOMBINATION/DNA / transposase / transpososome / BED domain / protein-DNA complex / RECOMBINATION-DNA complex | ||||||
Function / homology | ![]() nucleic acid metabolic process / protein dimerization activity / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||
![]() | Lannes, L. / Dyda, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding. Authors: Laurie Lannes / Christopher M Furman / Alison B Hickman / Fred Dyda / ![]() Abstract: The Hermes DNA transposon is a member of the eukaryotic hAT superfamily, and its transposase forms a ring-shaped tetramer of dimers. Our investigation, combining biochemical, crystallography and cryo- ...The Hermes DNA transposon is a member of the eukaryotic hAT superfamily, and its transposase forms a ring-shaped tetramer of dimers. Our investigation, combining biochemical, crystallography and cryo-electron microscopy, and in-cell assays, shows that the full-length Hermes octamer extensively interacts with its transposon left-end through multiple BED domains of three Hermes protomers contributed by three dimers explaining the role of the unusual higher-order assembly. By contrast, the right-end is bound to no BED domains at all. Thus, this work supports a model in which Hermes multimerizes to gather enough BED domains to find its left-end among the abundant genomic DNA, facilitating the subsequent interaction with the right-end. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 446.9 KB | Display | ![]() |
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PDB format | ![]() | 357.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 73 KB | Display | |
Data in CIF | ![]() | 108.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40553MC ![]() 8eb5C ![]() 8edgC 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: 70210.570 Da / Num. of mol.: 4 / Mutation: Q2E,K128G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 16909.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | Mass: 14197.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 2162.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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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 |
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Sample preparation
Component | Name: Two right-end Hermes transpososome / Type: COMPLEX Details: Hermes transposase tetramer of dimers complex bound to two transposon right-end DNAs. The complex was obtained by mixing the purified protein and the DNA. Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.627 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The complex was formed in vitro by mixing the purified protein with the DNA and further purified by size exclusion chromatography. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
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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 magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.66 sec. / Electron dose: 48.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9500 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2920000 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53656 Details: The 3D reconstruction is not representative of the complex in solution. The Hermes tranposase forms a tetramer of dimers assembled in a ring like shape. Only the Hermes dimers interacting ...Details: The 3D reconstruction is not representative of the complex in solution. The Hermes tranposase forms a tetramer of dimers assembled in a ring like shape. Only the Hermes dimers interacting with the DNAs have been partially reconstructed. Their BED domains did not show any density. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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