8HWB | pdb_00008hwb

D5 ATP-ADP-Apo-ssDNA IS2

PDB DOI: https://doi.org/10.2210/pdb8HWB/pdb
EM Map EMD-35052: EMDB EMDataResource
NAKB: 8HWB

Classification: VIRAL PROTEIN
Organism(s): Monkeypox virus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-12-29 Released: 2024-01-10
Deposition Author(s): Li, Y.N., Zhu, J., Guo, Y.Y., Yan, R.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus.

Li, Y., Zhu, J., Guo, Y., Yan, R.

(2024) Nat Struct Mol Biol 31: 68-81

PubMed: 38177671 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-023-01142-0
Primary Citation Related Structures:
8HWA, 8HWB, 8HWC, 8HWD, 8HWE, 8HWF, 8HWG, 8HWH

PubMed Abstract:
The Mpox pandemic, caused by the Mpox virus (or monkeypox virus, MPXV), has gained global attention. The D5 protein, a putative helicase-primase found in MPXV, plays a vital role in viral replication and genome uncoating. Here we determined multiple cryo-EM structures of full-length hexameric D5 in diverse states. These states were captured during ATP hydrolysis while moving along the single-stranded DNA (ssDNA) track. Through comprehensive structural analysis combined with the helicase activity system, we revealed that when the primase domain is truncated or the interaction between the primase and helicase domains is disrupted, the double-stranded DNA (dsDNA) unwinds into ssDNA, suggesting a critical regulatory role of the primase domain. Two transition states bound with ssDNA substrate during unwinding reveals that two ATP molecules were consumed to drive DNA moving forward two nucleotides. Collectively, our findings shed light on the molecular mechanism that links ATP hydrolysis to the DNA unwinding in poxviruses.

Organizational Affiliation

Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.

Macromolecule Content

Total Structure Weight: 638.17 kDa
Atom Count: 25,740
Modeled Residue Count: 3,153
Deposited Residue Count: 5,501
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primase D5	A B C D E A, B, C, D, E, F, H [auth K]	785	Monkeypox virus	Mutation(s): 0 Gene Names: 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... 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 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
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(PTPTPTPTPTPT)-3')	G [auth S]	6	Monkeypox virus
Sequence Annotations Expand
Reference Sequence

Small Molecules

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 R [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain R [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain R [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A], K [auth B], M [auth C], O [auth D], R [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] MOL2 format, chain Q [auth E] mmCIF format, chain Q [auth E]	Q [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth E] Interactions & Density Focus chain Q [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A], L [auth B], N [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D]