+Open data
-Basic information
Entry | Database: PDB / ID: 8hwc | ||||||
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Title | Cryo-EM Structure of D5 Apo | ||||||
Components | Primase D5 | ||||||
Keywords | VIRAL PROTEIN / MPVX | ||||||
Function / homology | 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. / hydrolase activity / P-loop containing nucleoside triphosphate hydrolase / Uncoating factor OPG117 Function and homology information | ||||||
Biological species | Monkeypox virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Li, Y.N. / Zhu, J. / Guo, Y.Y. / Yan, R.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hwc.cif.gz | 400.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hwc.ent.gz | 309.3 KB | Display | PDB format |
PDBx/mmJSON format | 8hwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hwc_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 8hwc_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 8hwc_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 8hwc_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/8hwc ftp://data.pdbj.org/pub/pdb/validation_reports/hw/8hwc | HTTPS FTP |
-Related structure data
Related structure data | 35053MC 8hwaC 8hwbC 8hwdC 8hweC 8hwfC 8hwgC 8hwhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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: Homo sapiens (human) / References: UniProt: Q5IXS3 |
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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 |
-Sample preparation
Component | Name: D5 Apo / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Monkeypox virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 779993 / Symmetry type: POINT |