[English] 日本語
Yorodumi
- PDB-2n2j: Solution structure of the EBNA-2 N-terminal Dimerization (END) do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n2j
TitleSolution structure of the EBNA-2 N-terminal Dimerization (END) domain from the Epstein-barr virus
ComponentsEpstein-Barr nuclear antigen 2
KeywordsVIRAL PROTEIN / HOMODIMER / END DOMAIN / EBNA-2
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / host cell nuclear matrix / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / protein serine/threonine phosphatase inhibitor activity / symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of DNA-templated transcription
Similarity search - Function
Epstein-Barr nuclear antigen 2
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsFriberg, A. / Sattler, M.
CitationJournal: Plos Pathog. / Year: 2015
Title: The EBNA-2 N-Terminal Transactivation Domain Folds into a Dimeric Structure Required for Target Gene Activation.
Authors: Friberg, A. / Thumann, S. / Hennig, J. / Zou, P. / Nossner, E. / Ling, P.D. / Sattler, M. / Kempkes, B.
History
DepositionMay 9, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epstein-Barr nuclear antigen 2
B: Epstein-Barr nuclear antigen 2


Theoretical massNumber of molelcules
Total (without water)13,3272
Polymers13,3272
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-19 kcal/mol
Surface area7730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1low energy and fewest violations

-
Components

#1: Protein Epstein-Barr nuclear antigen 2 / EBNA-2 / EBV nuclear antigen 2


Mass: 6663.451 Da / Num. of mol.: 2 / Fragment: END DOMAIN (UNP RESIDUES 1-58)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BYRF1, EBNA2 / Plasmid: PET-24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12978

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] EPSTEIN-BARR NUCLEAR ANTIGEN 2, 90% H2O/10% D2O90% H2O/10% D2O
20.1-0.5 mM [U-15N] EPSTEIN-BARR NUCLEAR ANTIGEN 2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1 mMEPSTEIN-BARR NUCLEAR ANTIGEN 2-1[U-13C; U-15N]1
mMEPSTEIN-BARR NUCLEAR ANTIGEN 2-2[U-15N]0.1-0.52
Sample conditionsIonic strength: 20 / pH: 6.9 / Pressure: AMBIENT / Temperature: 323 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503
Bruker AvanceBrukerAVANCE8004
Bruker AvanceBrukerAVANCE9505

-
Processing

NMR software
NameDeveloperClassification
CYANA_3.0Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection, processing
NMRViewJohnson, One Moon Scientificchemical shift assignment
SparkyGoddardchemical shift assignment
ARIA_2.2Linge, O'Donoghue and Nilgesrefinement
ARIA_2.2Linge, O'Donoghue and Nilgesprediction of dihedral angles
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: low energy and fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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://pdbjlvh1.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