[English] 日本語
Yorodumi
- PDB-2xy8: Paramagnetic-based NMR structure of the complex between the N- te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xy8
TitleParamagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III
Components
  • DNA POLYMERASE III SUBUNIT EPSILONDNA polymerase III holoenzyme
  • DNA POLYMERASE III SUBUNIT THETADNA polymerase III holoenzyme
KeywordsTRANSFERASE / DOCKING / EXPERIMENTAL RESTRAINTS / HADDOCK PROGRAM
Function / homology
Function and homology information


DNA polymerase III, core complex / DNA replication proofreading / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA replication ...DNA polymerase III, core complex / DNA replication proofreading / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / cytosol
Similarity search - Function
DNA polymerase III-theta / DNA polymerase III-theta, bacterial / DNA polymerase III-theta superfamily / DNA polymerase III, theta subunit / DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...DNA polymerase III-theta / DNA polymerase III-theta, bacterial / DNA polymerase III-theta superfamily / DNA polymerase III, theta subunit / DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit epsilon / DNA polymerase III subunit theta / DNA polymerase III subunit theta
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / DATA-DRIVEN FLEXIBLE DOCKING
AuthorsSchmitz, C. / Bonvin, A.M.J.J.
Citation
Journal: J.Biomol.NMR / Year: 2011
Title: Protein-Protein Haddocking Using Exclusively Pseudocontact Shifts.
Authors: Schmitz, C. / Bonvin, A.M.J.J.
#1: Journal: J.Biomol.NMR / Year: 2008
Title: Numbat: An Interactive Software Tool for Fitting Deltachi-Tensors to Molecular Coordinates Using Pseudocontact Shifts
Authors: Schmitz, C. / Stanton-Cook, M.J. / Su, X.C. / Otting, G. / Huber, T.
#2: Journal: J.Am.Chem.Soc. / Year: 2006
Title: Lanthanide Labeling Offers Fast NMR Approach to 3D Structure Determinations of Protein-Protein Complexes
Authors: Pintacuda, G. / Park, A.Y. / Keniry, M.A. / Dixon, N.E. / Otting, G.
#3: Journal: Proteins / Year: 2007
Title: Haddock Versus Haddock: New Features and Performance of Haddock2.0 On the Capri Targets.
Authors: de Vries, S.J. / van Dijk, A.D.J. / Krzeminski, M. / van Dijk, M. / Thureau, A. / Hsu, V. / Wassenaar, T. / Bonvin, A.M.J.J.
History
DepositionNov 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Version format compliance
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author / Item: _citation.page_last / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA POLYMERASE III SUBUNIT EPSILON
B: DNA POLYMERASE III SUBUNIT THETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6433
Polymers29,6032
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200TOP 10 STRUCTURES OF THE BEST CLUSTER
RepresentativeModel #1

-
Components

#1: Protein DNA POLYMERASE III SUBUNIT EPSILON / DNA polymerase III holoenzyme


Mass: 20741.689 Da / Num. of mol.: 1 / Fragment: EXONUCLEASE DOMAIN, RESIDUES 1-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03007, DNA-directed DNA polymerase
#2: Protein DNA POLYMERASE III SUBUNIT THETA / DNA polymerase III holoenzyme


Mass: 8861.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ABT0, UniProt: P0ABS8*PLUS, DNA-directed DNA polymerase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE COMPLEX WAS DOCKED USING PSEUDOCONTACT SHIFT ( PCS) RESTRAINTS.THE CONTENTS OF THE SAMPLE ARE SIMILAR TO THAT DESCRIBED IN LANTHANIDE LABELING OFFERS-FAST NMR APPROACH TO 3D STRUCTRE ...Text: THE COMPLEX WAS DOCKED USING PSEUDOCONTACT SHIFT ( PCS) RESTRAINTS.THE CONTENTS OF THE SAMPLE ARE SIMILAR TO THAT DESCRIBED IN LANTHANIDE LABELING OFFERS-FAST NMR APPROACH TO 3D STRUCTRE DETERMINATIONS OF PROTEIN-PROTEIN COMPLEXES. PINTACUDA ET ALL. JACS 2006

-
Sample preparation

Sample conditionspH: 7.2 / Pressure: 1 bar / Temperature: 298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2A.T.BRUNGER,P.D.ADAMS,G.M.CLORE, W.L.DELANO,P.GROS,R.W.GROSSE-KUNSTLEVE, J.-S.JIANG,J.KUSZEWSKI,M.NILGES,N.S.PANNU, R.J.READ,L.M.RICE,T.SIMONSON,G.L.WARRENrefinement
HADDOCK2.1-PARA BETABETADE VRIESstructure solution
RefinementMethod: DATA-DRIVEN FLEXIBLE DOCKING / Software ordinal: 1
Details: RUNNING WITHIN HADDOCK2.1-PARA BETA. REFINEMENT DETAILS CAN BE FOUND AT THE FOLLOWING PUBLICATION: DE VRIES ET AL. PROTEINS 2007 (REFERENCE 3 IN REMARK 1).
NMR ensembleConformer selection criteria: TOP 10 STRUCTURES OF THE BEST CLUSTER
Conformers calculated total number: 200 / 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://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