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- PDB-7u1t: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element -

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Basic information

Entry
Database: PDB / ID: 7u1t
TitleEBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element
Components
  • (DNA (59-MER)) x 2
  • Epstein-Barr nuclear antigen 1
KeywordsVIRAL PROTEIN/DNA / EBV latency protein EBNA1 Dyad symmetry / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


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
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMei, Y. / Lieberman, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA093606-18 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE017336-13 United States
CitationJournal: To Be Published
Title: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element
Authors: Mei, Y. / Lieberman, P.
History
DepositionFeb 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epstein-Barr nuclear antigen 1
B: Epstein-Barr nuclear antigen 1
C: Epstein-Barr nuclear antigen 1
D: Epstein-Barr nuclear antigen 1
E: DNA (59-MER)
F: DNA (59-MER)


Theoretical massNumber of molelcules
Total (without water)113,3326
Polymers113,3326
Non-polymers00
Water00
1


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

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Components

#1: Protein
Epstein-Barr nuclear antigen 1 / EBNA-1 / EBV nuclear antigen 1


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.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: EBNA1, BKRF1 / Plasmid: pET-mod / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) / References: UniProt: P03211
#2: DNA chain DNA (59-MER)


Mass: 18181.674 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
References: GenBank: 330330
#3: DNA chain DNA (59-MER)


Mass: 18177.703 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
References: GenBank: 330330

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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: EBNA1 DNA binding domain binds to half Dyad Symmetry region
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.160 MDa / Experimental value: NO
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta(DE3) / Plasmid: pET-mod
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
2100 mMsodium chlorideNaCl1
32 mMtris(2-carboxyethyl)phosphine1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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
IDNameVersionCategoryDetails
2RELION3.1.3particle selection
5cryoSPARC3.3.1CTF correctionPatch CTF(M)
6RELION3.1.3CTF correctionCTFFIND4.1
9UCSF Chimera8.6.9model fitting
10Coot0.9.6model fitting
14RELION3.1.3classification
15RELION3.1.33D reconstruction
16PHENIX1.2model refinement
17Coot0.9.6model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1806607
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168682 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB 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

6pw2

/ Source name: PDB / Type: experimental model

IDPdb chain-IDPdb chain residue range
1A461-607
2B461-607
3C461-607
4D461-607
5E3-57
6F3-57

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