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- PDB-7u1t: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u1t | |||||||||
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Title | EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element | |||||||||
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![]() | VIRAL PROTEIN/DNA / EBV latency protein EBNA1 Dyad symmetry / VIRAL PROTEIN-DNA complex | |||||||||
Function / homology | ![]() host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response / positive regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Mei, Y. / Lieberman, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element Authors: Mei, Y. / Lieberman, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.9 KB | Display | ![]() |
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PDB format | ![]() | 149.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 820.7 KB | Display | ![]() |
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Full document | ![]() | 886.8 KB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 60.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26305MC 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: 19243.031 Da / Num. of mol.: 4 / Fragment: DNA-binding domain (UNP residues 438-615) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: B95-8 / Gene: EBNA1, BKRF1 / Plasmid: pET-mod / Production host: ![]() ![]() #2: DNA chain | | Mass: 18181.674 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() References: GenBank: 330330 #3: DNA chain | | Mass: 18177.703 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() References: GenBank: 330330 |
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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: EBNA1 DNA binding domain binds to half Dyad Symmetry region Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.160 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 21 % / Chamber temperature: 293 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 30000 nm / Nominal defocus min: 10000 nm / Calibrated defocus min: 10000 nm / Calibrated defocus max: 30000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.68 sec. / Electron dose: 1.03 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4938 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1806607 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168682 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 135 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 6PW2 / Initial refinement model-ID: 1 / PDB-ID: 6PW2 / Source name: PDB / Type: experimental model
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