[English] 日本語
Yorodumi
- PDB-9k9t: MPXV DNA polymerase in complex with CDV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k9t
TitleMPXV DNA polymerase in complex with CDV
Components
  • DNA (24-MER)
  • DNA (38-MER)
  • DNA polymerase
  • DNA polymerase processivity factor component A20
  • E4R
KeywordsREPLICATION/DNA / complex / replicate / DNA / mpox / polymerase / REPLICATION-DNA complex
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / viral DNA genome replication / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / DNA repair / nucleotide binding / DNA binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / : ...DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase / DNA polymerase processivity factor / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsXie, Y.F. / Kuai, L. / Peng, Q. / Wang, Q. / Wang, H. / Li, X.M. / Qi, J.X. / Ding, Q. / Shi, Y. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: MPXV DNA polymerase in complex with CDV
Authors: Xie, Y.F. / Kuai, L. / Peng, Q. / Wang, Q. / Wang, H. / Li, X.M. / Qi, J.X. / Ding, Q. / Shi, Y. / Gao, F.
History
DepositionOct 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase
E: DNA (38-MER)
P: DNA (24-MER)
C: DNA polymerase processivity factor component A20
B: E4R


Theoretical massNumber of molelcules
Total (without water)213,2195
Polymers213,2195
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein DNA polymerase


Mass: 119837.016 Da / Num. of mol.: 1 / Mutation: D166A,E168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG071, POL, MPXVgp056 / Production host: Spodoptera (butterflies/moths)
References: UniProt: A0A7H0DN44, DNA-directed DNA polymerase
#2: DNA chain DNA (38-MER)


Mass: 11677.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Monkeypox virus
#3: DNA chain DNA (24-MER)


Mass: 7392.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Monkeypox virus
#4: Protein DNA polymerase processivity factor component A20


Mass: 49203.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: A22R, MPXV-COP-126, MPXV-M2940_FCT-131, MPXV-M2957_Lagos-131, MPXV-M3021_Delta-131, MPXV-M5320_M15_Bayelsa-124, MPXV-Nig_SEV71_2_82-126, MPXV-PCH-128, MPXV-Singapore-131, MPXV-SL-126, MPXV-UK_ ...Gene: A22R, MPXV-COP-126, MPXV-M2940_FCT-131, MPXV-M2957_Lagos-131, MPXV-M3021_Delta-131, MPXV-M5320_M15_Bayelsa-124, MPXV-Nig_SEV71_2_82-126, MPXV-PCH-128, MPXV-Singapore-131, MPXV-SL-126, MPXV-UK_P1-131, MPXV-UK_P2-131, MPXV-UK_P3-131, MPXV-USA2003_099_GR-131, MPXV-USA2003_206_DM-131, MPXV-USA2003_223_RS-131, MPXV-UTC-122, MPXV-W_Nigeria-126, MPXV-WRAIR126, MPXV297957_122, MPXV298464_113, MPXV_LIB1970_184_138, MPXV_USA2003_039_138, MPXV_USA2003_044_138, PDLMKLCO_00135
Production host: Spodoptera (butterflies/moths) / References: UniProt: Q5IXP2
#5: Protein E4R / MPXV-COP-095 / MPXV-SL-095 / MPXV-WRAIR095 / MPXVgp101 / Uracil-DNA glycosylase / Uracil-DNA ...MPXV-COP-095 / MPXV-SL-095 / MPXV-WRAIR095 / MPXVgp101 / Uracil-DNA glycosylase / Uracil-DNA glycosylase DNA polymerase / Uracil-DNA glycosylase interacts with A20R / DNA polymerase processivity factor


Mass: 25107.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: E4R, UNG, MPXV-CAM1990_02-093, MPXV-Congo_8-094, MPXV-COP-095, MPXV-GAB1988_001-094, MPXV-Ikubi-093, MPXV-M2940_FCT-099, MPXV-M2957_Lagos-099, MPXV-M3021_Delta-099, MPXV-M5320_M15_Bayelsa-092, ...Gene: E4R, UNG, MPXV-CAM1990_02-093, MPXV-Congo_8-094, MPXV-COP-095, MPXV-GAB1988_001-094, MPXV-Ikubi-093, MPXV-M2940_FCT-099, MPXV-M2957_Lagos-099, MPXV-M3021_Delta-099, MPXV-M5320_M15_Bayelsa-092, MPXV-Nig_SEV71_2_82-094, MPXV-PCH-096, MPXV-Singapore-099, MPXV-SL-095, MPXV-UK_P1-099, MPXV-UK_P2-099, MPXV-UK_P3-099, MPXV-USA2003_099_GR-099, MPXV-USA2003_206_DM-099, MPXV-USA2003_223_RS-099, MPXV-UTC-090, MPXV-W_Nigeria-094, MPXV-WRAIR095, MPXV297957_090, MPXV298464_081, MPXV_DRC_Yandongi_102, MPXV_LIB1970_184_106, MPXV_RCG2003_358_106, MPXV_SUD2005_01_102, MPXV_USA2003_039_106, MPXV_USA2003_044_106, MPXV_ZAI1979_005_106, MPXVgp101, PDLMKLCO_00104
Production host: Spodoptera (butterflies/moths) / References: UniProt: Q5IXS4, uracil-DNA glycosylase
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: MPXV DNA polymerase in complex with primer/4U template DNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52654 / Symmetry type: POINT
RefinementHighest resolution: 2.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314531
ELECTRON MICROSCOPYf_angle_d0.63619819
ELECTRON MICROSCOPYf_dihedral_angle_d14.2272216
ELECTRON MICROSCOPYf_chiral_restr0.0452197
ELECTRON MICROSCOPYf_plane_restr0.0042369

+
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