[English] 日本語
Yorodumi
- PDB-6zxp: Solution structure of the C-terminal domain of the vaccinia virus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zxp
TitleSolution structure of the C-terminal domain of the vaccinia virus DNA polymerase processivity factor component A20 fused to a short peptide from the viral DNA polymerase E9.
ComponentsDNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9
KeywordsREPLICATION / Poxviridae / DNA polymerase holoenzyme / processivity factor binding
Function / homologyChordopoxvirus A20R / Chordopoxvirus A20R protein / viral DNA genome replication / DNA replication / DNA polymerase processivity factor component OPG148
Function and homology information
Biological speciesVaccinia virus Copenhagen
MethodSOLUTION NMR / molecular dynamics
AuthorsBersch, B. / Tarbouriech, N. / Burmeister, W. / Iseni, F.
Citation
Journal: J.Mol.Biol. / Year: 2021
Title: Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor.
Authors: Bersch, B. / Tarbouriech, N. / Burmeister, W.P. / Iseni, F.
#1: Journal: Nature Communications / Year: 2017
Title: The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.
Authors: Tarbouriech, N. / Ducournau, C. / Hutin, S. / Mas, P.J. / Man, P. / Forest, E. / Hart, D.J. / Peyrefitte, C.N. / Burmeister, W. / Iseni, F.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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: DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9


Theoretical massNumber of molelcules
Total (without water)16,8831
Polymers16,8831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8440 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein DNA polymerase processivity factor component A20,DNA polymerase processivity factor component E9


Mass: 16882.934 Da / Num. of mol.: 1 / Mutation: L147A
Source method: isolated from a genetically manipulated source
Details: This is a recombinant fusion protein: residues 2-124 correspond to A20_VACCC:304-426, residues 125-135 to a flexible linker and residues 136-150 to E9_VACCC:576-590. E9_VACCC:L587A ...Details: This is a recombinant fusion protein: residues 2-124 correspond to A20_VACCC:304-426, residues 125-135 to a flexible linker and residues 136-150 to E9_VACCC:576-590. E9_VACCC:L587A mutation,This is a recombinant fusion protein: residues 2-124 correspond to A20_VACCC:304-426, residues 125-135 to a flexible linker and residues 136-150 to E9_VACCC:576-590. E9_VACCC:L587A mutation
Source: (gene. exp.) Vaccinia virus Copenhagen / Gene: A20R / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Star / References: UniProt: P20995

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic115N-TROSY
122isotropic113C-HSQC
133isotropic12D-TOCSY
142isotropic13D HNCO
152isotropic13D HN(CA)CB
1112isotropic13D HN(COCA)CB
1102isotropic13D (H)CCH-TOCSY
191isotropic13D-15N-edited NOESY
182isotropic13D-13C edited NOESY
172isotropic13D-13C-13C methyl NOESY
163isotropic12D NOESY
1141isotropic215N-R1
1131isotropic215N-R2
1121isotropic215N hetNOE

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-15N] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O3 mm tube15N-H2O90% H2O/10% D2O
solution20.8 mM [U-15N13C] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O3 mm tube15N13C-H2O90% H2O/10% D2O
solution31 mM [U-15N13C] A20-i3, 50 mM potassium phosphate, 300 mM NaCl, 1.2 mM TCEP, 90% H2O/10% D2O3 mm tube15N-D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMA20-i3[U-15N]1
50 mMpotassium phosphatenatural abundance1
300 mMNaClnatural abundance1
1.2 mMTCEPnatural abundance1
0.8 mMA20-i3[U-15N13C]2
50 mMpotassium phosphatenatural abundance2
300 mMNaClnatural abundance2
1.2 mMTCEPnatural abundance2
1 mMA20-i3[U-15N13C]3
50 mMpotassium phosphatenatural abundance3
300 mMNaClnatural abundance3
1.2 mMTCEPnatural abundance3
Sample conditionsDetails: 3 mm tube / Ionic strength: 0.3 M / Label: general / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.5

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9501
Bruker AVANCEBrukerAVANCE7002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
UNIOTorsten Herrmannpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 6 / Details: in explicit water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

+
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