8WH2 | pdb_00008wh2

Deposited: 2023-09-22 Released: 2024-11-27
Deposition Author(s): Zhang, Z., Dong, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

(2024) Sci Adv 10: eadl1150-eadl1150

PubMed Abstract:
An outbreak of mpox virus in May 2022 has spread over 110 nonpandemic regions in the world, posing a great threat to global health. Mpox virus E5, a helicase-primase, plays an essential role in DNA replication, but the molecular mechanisms are elusive. Here, we report seven structures of mpox virus E5 in a double hexamer (DH) and six in single hexamer in different conformations, indicating a rotation mechanism for helicase and a coupling action for primase. The DH is formed through the interface of zinc-binding domains, and the central channel density indicates potential double-stranded DNA (dsDNA), which helps to identify dsDNA binding residues Arg ²⁴⁹, Lys ²⁸⁶, Lys ³¹⁵, and Lys ³¹⁷. Our work is important not only for understanding poxviral DNA replication but also for the development of novel therapeutics for serious poxviral infections including smallpox virus and mpox virus.

Organizational Affiliation

Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncoating factor OPG117	A, B, C, D, E A, B, C, D, E, F	785	Monkeypox virus	Mutation(s): 0 Gene Names: E5R EC: 3.6.4
UniProt
Find proteins for A0A7H0DN89 (Monkeypox virus) Explore A0A7H0DN89 Go to UniProtKB: A0A7H0DN89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7H0DN89
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(PCPCPCPCP*C)-3')	G [auth T]	5	Spodoptera frugiperda
Sequence Annotations Expand
Reference Sequence

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth D] MOL2 format, chain L [auth F] MOL2 format, chain K [auth D] mmCIF format, chain L [auth F] mmCIF format, chain K [auth D]	K [auth D], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth D] Focus chain L [auth F] Interactions & Density Focus chain K [auth D] Focus chain L [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]