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Open data
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Basic information
Entry | Database: PDB / ID: 8hwb | ||||||
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Title | D5 ATP-ADP-Apo-ssDNA IS2 | ||||||
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![]() | VIRAL PROTEIN / MPVX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Li, Y.N. / Zhu, J. / Guo, Y.Y. / Yan, R.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus. Authors: Yaning Li / Jing Zhu / Yingying Guo / Renhong Yan / ![]() 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 ...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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 590.6 KB | Display | ![]() |
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PDB format | ![]() | 471.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 816.2 KB | Display | ![]() |
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Full document | ![]() | 860 KB | Display | |
Data in XML | ![]() | 64 KB | Display | |
Data in CIF | ![]() | 93.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35052MC ![]() 8hwaC ![]() 8hwcC ![]() 8hwdC ![]() 8hweC ![]() 8hwfC ![]() 8hwgC ![]() 8hwhC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 90476.344 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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: ![]() #2: DNA chain | | Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ADP / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: D5 ATP-ADP-Apo-ssDNA IS2 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: RELION / Version: 3.0.6 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67228 / Symmetry type: POINT |