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- EMDB-26305: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26305
TitleEBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element
Map data
Sample
  • Complex: EBNA1 DNA binding domain binds to half Dyad Symmetry region
    • Protein or peptide: Epstein-Barr nuclear antigen 1
    • DNA: DNA (59-MER)
    • DNA: DNA (59-MER)
KeywordsEBV 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
Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMei Y / Lieberman P
Funding support United States, 2 items
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, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26305.png

Downloads & links

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Map

FileDownload / File: emd_26305.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.014781157 - 0.044196803
Average (Standard dev.)0.000054378732 (±0.001144742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : EBNA1 DNA binding domain binds to half Dyad Symmetry region

EntireName: EBNA1 DNA binding domain binds to half Dyad Symmetry region
Components
  • Complex: EBNA1 DNA binding domain binds to half Dyad Symmetry region
    • Protein or peptide: Epstein-Barr nuclear antigen 1
    • DNA: DNA (59-MER)
    • DNA: DNA (59-MER)

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Supramolecule #1: EBNA1 DNA binding domain binds to half Dyad Symmetry region

SupramoleculeName: EBNA1 DNA binding domain binds to half Dyad Symmetry region
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Epstein-Barr nuclear antigen 1

MacromoleculeName: Epstein-Barr nuclear antigen 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 19.243031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PADDPGEGPS TGPRGQGDGG RRKKGGWFGK HRGQGGSNPK FENIAEGLRA LLARSHVERT TDEGTWVAGV FVYGGSKTSL YNLRRGTAL AIPQCRLTPL SRLPFGMAPG PGPQPGPLRE SIVCYFMVFL QTHIFAEVLK DAIKDLVMTK PAPTCNIRVT V CSFDDGVD LPPWFPPMVE

UniProtKB: Epstein-Barr nuclear antigen 1

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Macromolecule #2: DNA (59-MER)

MacromoleculeName: DNA (59-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Molecular weightTheoretical: 18.181674 KDa
SequenceString: (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DT)(DA)(DG)(DC)(DA)(DT) (DA)(DT)(DG)(DC)(DT)(DT)(DC)(DC)(DC) (DG)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DA)(DC) (DA) (DT)(DA)(DT)(DG)(DC)(DT) ...String:
(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DT)(DA)(DG)(DC)(DA)(DT) (DA)(DT)(DG)(DC)(DT)(DT)(DC)(DC)(DC) (DG)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DA)(DC) (DA) (DT)(DA)(DT)(DG)(DC)(DT)(DA)(DT) (DT)(DG)(DA)(DA)(DT)(DT)(DA)(DG)(DG)(DG) (DT)

GENBANK: GENBANK: M80517.1

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Macromolecule #3: DNA (59-MER)

MacromoleculeName: DNA (59-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Molecular weightTheoretical: 18.177703 KDa
SequenceString: (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DT) (DG)(DT)(DT)(DA)(DC)(DC)(DC)(DA)(DA) (DC)(DG)(DG)(DG)(DA)(DA)(DG)(DC)(DA)(DT) (DA) (DT)(DG)(DC)(DT)(DA)(DT) ...String:
(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DT) (DG)(DT)(DT)(DA)(DC)(DC)(DC)(DA)(DA) (DC)(DG)(DG)(DG)(DA)(DA)(DG)(DC)(DA)(DT) (DA) (DT)(DG)(DC)(DT)(DA)(DT)(DC)(DG) (DA)(DA)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)

GENBANK: GENBANK: M80517.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMsodium chlorideNaCl
2.0 mMtris(2-carboxyethyl)phosphine
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 30.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 21 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4938 / Average exposure time: 1.68 sec. / Average electron dose: 1.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 30.0 µm / Calibrated defocus min: 10.0 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 30.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1806607
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6pw2

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 168682
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Avg.num./class: 168682 / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6pw2

chain_id: A, residue_range: 461-607, source_name: PDB, initial_model_type: experimental model

6pw2

chain_id: B, residue_range: 461-607, source_name: PDB, initial_model_type: experimental model

6pw2

chain_id: C, residue_range: 461-607, source_name: PDB, initial_model_type: experimental model

6pw2

chain_id: D, residue_range: 461-607, source_name: PDB, initial_model_type: experimental model

6pw2

chain_id: E, residue_range: 3-57, source_name: PDB, initial_model_type: experimental model

6pw2

chain_id: F, residue_range: 3-57, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 135
Output model

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

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