[English] 日本語
Yorodumi
- EMDB-27500: EBNA1 DNA binding domain (DBD) (458-617)+2 repeats of family repe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27500
TitleEBNA1 DNA binding domain (DBD) (458-617)+2 repeats of family repeat (FR) region
Map data
Sample
  • Complex: EBNA1 DBD+2XFR complex
    • Protein or peptide: Epstein-Barr nuclear antigen 1Epstein–Barr virus nuclear antigen 1
    • DNA: 2XFR DNA (56-MER)
    • DNA: 2XFR DNA (56-MER)
  • Ligand: water
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 / virus-mediated perturbation of host defense response / endonuclease activity / DNA-binding transcription factor activity ...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 / virus-mediated perturbation of host defense response / endonuclease activity / DNA-binding transcription factor activity / 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: 3.23 Å
AuthorsMei Y / Lieberman PM / Murakami K
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)RO1 CA093606 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)RO1 CA259171 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1-GM123233 United States
National Science Foundation (NSF, United States)MCB 2131806 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA0101815 United States
CitationJournal: J Virol / Year: 2022
Title: Cryo-EM Structure and Functional Studies of EBNA1 Binding to the Family of Repeats and Dyad Symmetry Elements of Epstein-Barr Virus .
Authors: Yang Mei / Troy E Messick / Jayaraju Dheekollu / Hee Jong Kim / Sudheer Molugu / Leonardo Josué Castro Muñoz / Vera Moiskeenkova-Bell / Kenji Murakami / Paul M Lieberman /
Abstract: Epstein-Barr nuclear antigen 1 (EBNA1) is a multifunctional viral-encoded DNA-binding protein essential for Epstein-Barr virus (EBV) DNA replication and episome maintenance. EBNA1 binds to two ...Epstein-Barr nuclear antigen 1 (EBNA1) is a multifunctional viral-encoded DNA-binding protein essential for Epstein-Barr virus (EBV) DNA replication and episome maintenance. EBNA1 binds to two functionally distinct elements at the viral origin of plasmid replication (), termed the dyad symmetry (DS) element, required for replication initiation and the family of repeats (FR) required for episome maintenance. Here, we determined the cryo-electron microscopy (cryo-EM) structure of the EBNA1 DNA binding domain (DBD) from amino acids (aa) 459 to 614 and its interaction with two tandem sites at the DS and FR. We found that EBNA1 induces a strong DNA bending angle in the DS, while the FR is more linear. The N-terminal arm of the DBD (aa 444 to 468) makes extensive contact with DNA as it wraps around the minor groove, with some conformational variation among EBNA1 monomers. Mutation of variable-contact residues K460 and K461 had only minor effects on DNA binding but had abrogated -dependent DNA replication. We also observed that the AT-rich intervening DNA between EBNA1 binding sites in the FR can be occupied by the EBNA1 AT hook, N-terminal domain (NTD) aa 1 to 90 to form a Zn-dependent stable complex with EBNA1 DBD on a 2×FR DNA template. We propose a model showing EBNA1 DBD and NTD cobinding at the FR and suggest that this may contribute to the oligomerization of viral episomes important for maintenance during latent infection. EBV latent infection is causally linked to diverse cancers and autoimmune disorders. EBNA1 is the viral-encoded DNA binding protein required for episomal maintenance during latent infection and is consistently expressed in all EBV tumors. The interaction of EBNA1 with different genetic elements confers different viral functions, such as replication initiation at DS and chromosome tethering at FR. Here, we used cryo-EM to determine the structure of the EBNA1 DNA-binding domain (DBD) bound to two tandem sites at the DS and at the FR. We also show that the NTD of EBNA1 can interact with the AT-rich DNA sequence between tandem EBNA1 DBD binding sites in the FR. These results provide new information on the mechanism of EBNA1 DNA binding at DS and FR and suggest a higher-order oligomeric structure of EBNA1 bound to FR. Our findings have implications for targeting EBNA1 in EBV-associated disease.
History
DepositionJul 7, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27500.png

Downloads & links

-
Map

FileDownload / File: emd_27500.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0694 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.13081452 - 0.18040057
Average (Standard dev.)0.0001787841 (±0.00300271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.65598 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_27500_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27500_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EBNA1 DBD+2XFR complex

EntireName: EBNA1 DBD+2XFR complex
Components
  • Complex: EBNA1 DBD+2XFR complex
    • Protein or peptide: Epstein-Barr nuclear antigen 1Epstein–Barr virus nuclear antigen 1
    • DNA: 2XFR DNA (56-MER)
    • DNA: 2XFR DNA (56-MER)
  • Ligand: water

-
Supramolecule #1: EBNA1 DBD+2XFR complex

SupramoleculeName: EBNA1 DBD+2XFR complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))

-
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: 17.564369 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
RRKKGGWFGK HRGQGGSNPK FENIAEGLRA LLARSHVERT TDEGTWVAGV FVYGGSKTSL YNLRRGTALA IPQCRLTPLS RLPFGMAPG PGPQPGPLRE SIVCYFMVFL QTHIFAEVLK DAIKDLVMTK PAPTCNIRVT VCSFDDGVDL PPWFPPMVEG A

-
Macromolecule #2: 2XFR DNA (56-MER)

MacromoleculeName: 2XFR DNA (56-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: 17.241064 KDa
SequenceString: (DA)(DT)(DC)(DT)(DG)(DG)(DG)(DT)(DA)(DG) (DT)(DA)(DT)(DA)(DT)(DG)(DC)(DT)(DA)(DT) (DC)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DA) (DT)(DA)(DT)(DC)(DT)(DG)(DG)(DG)(DT)(DA) (DG) (DC)(DA)(DT)(DA)(DG)(DG) ...String:
(DA)(DT)(DC)(DT)(DG)(DG)(DG)(DT)(DA)(DG) (DT)(DA)(DT)(DA)(DT)(DG)(DC)(DT)(DA)(DT) (DC)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DA) (DT)(DA)(DT)(DC)(DT)(DG)(DG)(DG)(DT)(DA) (DG) (DC)(DA)(DT)(DA)(DG)(DG)(DC)(DT) (DA)(DT)(DC)(DC)(DT)(DA)(DT)(DC)

-
Macromolecule #3: 2XFR DNA (56-MER)

MacromoleculeName: 2XFR DNA (56-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: 17.264139 KDa
SequenceString: (DG)(DA)(DT)(DA)(DG)(DG)(DA)(DT)(DA)(DG) (DC)(DC)(DT)(DA)(DT)(DG)(DC)(DT)(DA)(DC) (DC)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DA)(DA)(DT)(DT)(DA)(DG)(DG)(DA)(DT)(DA) (DG) (DC)(DA)(DT)(DA)(DT)(DA) ...String:
(DG)(DA)(DT)(DA)(DG)(DG)(DA)(DT)(DA)(DG) (DC)(DC)(DT)(DA)(DT)(DG)(DC)(DT)(DA)(DC) (DC)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DA)(DA)(DT)(DT)(DA)(DG)(DG)(DA)(DT)(DA) (DG) (DC)(DA)(DT)(DA)(DT)(DA)(DC)(DT) (DA)(DC)(DC)(DC)(DA)(DG)(DA)(DT)

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClSodium chloridesodium chloride
2.0 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 22 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 10.0 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5300 / Average exposure time: 4.0 sec. / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1242375

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8dlf:
EBNA1 DNA binding domain (DBD) (458-617)+2 repeats of family repeat (FR) region

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more