[English] 日本語
Yorodumi
- PDB-5t7x: Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-deri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t7x
TitleCrystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA
Components
  • DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')
  • Epstein-Barr nuclear antigen 1
KeywordsDNA BINDING PROTEIN/DNA / Dimer / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA replication / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMalecka, K.A. / Messick, T.E. / Lieberman, P.M.
CitationJournal: Oncotarget / Year: 2017
Title: Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency.
Authors: Dheekollu, J. / Malecka, K. / Wiedmer, A. / Delecluse, H.J. / Chiang, A.K. / Altieri, D.C. / Messick, T.E. / Lieberman, P.M.
History
DepositionSep 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')
A: Epstein-Barr nuclear antigen 1
B: Epstein-Barr nuclear antigen 1


Theoretical massNumber of molelcules
Total (without water)43,6974
Polymers43,6974
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-56 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.025, 64.904, 111.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')


Mass: 5476.554 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
#2: DNA chain DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')


Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
#3: Protein Epstein-Barr nuclear antigen 1 / EBV nuclear antigen 1


Mass: 16332.018 Da / Num. of mol.: 2 / Fragment: UNP residues 459-507
Source method: isolated from a genetically manipulated source
Details: patient-derived, nasopharyngeal carcinoma
Source: (gene. exp.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: GD1 / Gene: EBNA1, BKRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KSS4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium acetate, 0.15 M magnesium acetate tetrahydrate, 0.05 M Hepes, pH 7.0, 5% PEG 4000
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19350 / % possible obs: 98.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 21.9
Reflection shellRedundancy: 7.2 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 7.4 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B3T

1b3t


Resolution: 2.35→23.373 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2329 2183 9.99 %
Rwork0.1854 --
obs0.1902 21843 62.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→23.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 732 0 122 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053150
X-RAY DIFFRACTIONf_angle_d0.9054421
X-RAY DIFFRACTIONf_dihedral_angle_d20.0591219
X-RAY DIFFRACTIONf_chiral_restr0.036486
X-RAY DIFFRACTIONf_plane_restr0.005449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.40120.3098480.2716453X-RAY DIFFRACTION23
2.4012-2.4570.3274680.2852565X-RAY DIFFRACTION29
2.457-2.51840.321830.2977706X-RAY DIFFRACTION36
2.5184-2.58640.3714930.2971929X-RAY DIFFRACTION46
2.5864-2.66240.2951030.3107984X-RAY DIFFRACTION51
2.6624-2.74820.34881230.30591084X-RAY DIFFRACTION54
2.7482-2.84620.29761270.31781099X-RAY DIFFRACTION56
2.8462-2.960.3441330.2841160X-RAY DIFFRACTION59
2.96-3.09440.31831370.23041267X-RAY DIFFRACTION64
3.0944-3.25710.28281510.22391332X-RAY DIFFRACTION68
3.2571-3.46060.25371590.19511425X-RAY DIFFRACTION73
3.4606-3.72680.19321840.15871627X-RAY DIFFRACTION82
3.7268-4.10.1731880.1361665X-RAY DIFFRACTION84
4.1-4.68920.16561960.12341758X-RAY DIFFRACTION89
4.6892-5.89220.17381890.12521774X-RAY DIFFRACTION89
5.8922-23.37450.20532010.13951832X-RAY DIFFRACTION93

+
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