[English] 日本語
Yorodumi
- PDB-9im2: The Cryo-EM structure of MPXV E5 in complex with ssDNA in interme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9im2
TitleThe Cryo-EM structure of MPXV E5 in complex with ssDNA in intermediate state 3
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
  • Primase D5
KeywordsVIRAL PROTEIN/DNA / complex / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


helicase activity / hydrolase activity
Similarity search - Function
DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / : / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / Uncoating factor OPG117
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsCheng, Y.X. / Han, P. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: Nat Commun / Year: 2025
Title: Assembly and breakage of head-to-head double hexamer reveals mpox virus E5-catalyzed DNA unwinding initiation.
Authors: Yingxian Cheng / Pu Han / Qi Peng / Ruili Liu / Hao Liu / Bin Yuan / Yunfei Zhao / Lu Kuai / Jianxun Qi / Kai Miao / Yi Shi / George Fu Gao / Han Wang /
Abstract: The replicative helicase-catalyzed unwinding of the DNA double helix is the initiation of DNA replication. Helicases and primases are functionally related enzymes that have even been expressed as ...The replicative helicase-catalyzed unwinding of the DNA double helix is the initiation of DNA replication. Helicases and primases are functionally related enzymes that have even been expressed as fusion proteins in some organisms and viruses. However, the mechanism underlying DNA unwinding initiation by these helicase-primase fusion enzymes and the functional association between domains have not been elucidated. Herein, we report the cryo-EM structures of mpox virus E5, the founding member of these helicase-primase enzymes, in various enzymatic stages. Notably, E5 forms a head-to-head double hexamer encircling dsDNA, disrupted by the conformational rearrangement of primase domains upon nucleotide incorporation. Five E5-ssDNA-ATP structures further support an ATP cycle-driven non-classical escort model for E5 translocation. Finally, the helicase domain is found to enhance the primase function as a DNA scaffold. Together, our data shed light on the E5-mediated DNA unwinding model including dsDNA loading, DNA melting, ssDNA translocation, and provide a reasonable interpretation for evolutionary preservation of helicase-primase fusion from a functional perspective.
History
DepositionJul 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Primase D5
F: Primase D5
A: Primase D5
B: Primase D5
C: Primase D5
D: Primase D5
X: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,31115
Polymers544,9427
Non-polymers2,3698
Water00
1


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

-
Components

-
Protein / DNA chain , 2 types, 7 molecules EFABCDX

#1: Protein
Primase D5


Mass: 90476.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: E5R, MPXV-COP-096, MPXV-M2940_FCT-100, MPXV-M2957_Lagos-100, MPXV-M3021_Delta-100, MPXV-M5320_M15_Bayelsa-093, MPXV-Nig_SEV71_2_82-095, MPXV-PCH-097, MPXV-Singapore-100, MPXV-SL-096, MPXV-UK_P1- ...Gene: E5R, MPXV-COP-096, MPXV-M2940_FCT-100, MPXV-M2957_Lagos-100, MPXV-M3021_Delta-100, MPXV-M5320_M15_Bayelsa-093, MPXV-Nig_SEV71_2_82-095, MPXV-PCH-097, MPXV-Singapore-100, MPXV-SL-096, MPXV-UK_P1-100, MPXV-UK_P2-100, MPXV-UK_P3-100, MPXV-USA2003_099_GR-100, MPXV-USA2003_206_DM-100, MPXV-USA2003_223_RS-100, MPXV-UTC-091, MPXV-W_Nigeria-095, MPXV-WRAIR096, MPXV298464_082, MPXV_LIB1970_184_107, MPXV_USA2003_039_107, MPXV_USA2003_044_107, PDLMKLCO_00105
Production host: Spodoptera (butterflies/moths) / References: UniProt: Q5IXS3
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2084.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Production host: Spodoptera (butterflies/moths)

-
Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: MPXV E5 in complex with ssDNA in intermediate state 3 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109348 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226375
ELECTRON MICROSCOPYf_angle_d0.52935706
ELECTRON MICROSCOPYf_dihedral_angle_d7.353522
ELECTRON MICROSCOPYf_chiral_restr0.044005
ELECTRON MICROSCOPYf_plane_restr0.0034517

+
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