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Yorodumi- PDB-8j8f: Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j8f | ||||||
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Title | Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and dCTP | ||||||
Components |
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Keywords | VIRAL PROTEIN / Monkeypox virus / DNA replication holoenzyme / DNA replication machinery / DNA polymerase / B-family DNA polymerase / uracil-DNA glycosylase / MPXV / orthopoxvirus / poxviridae / DNA processivity factor | ||||||
Function / homology | Function and homology information viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / base-excision repair, gap-filling / DNA replication / DNA recombination / DNA-directed DNA polymerase ...viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / base-excision repair, gap-filling / DNA replication / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Monkeypox virus DNA molecule (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||
Authors | Xu, Y. / Wu, Y. / Wu, X. / Zhang, Y. / Yang, Y. / Li, D. / Yang, B. / Gao, K. / Zhang, Z. / Dong, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Biol Macromol / Year: 2024 Title: Structural basis of human mpox viral DNA replication inhibition by brincidofovir and cidofovir. Authors: Yunxia Xu / Yaqi Wu / Xiaoying Wu / Yuanyuan Zhang / Yaxue Yang / Danyang Li / Biao Yang / Kaiting Gao / Zhengyu Zhang / Changjiang Dong / Abstract: Mpox virus has wildly spread over 108 non-endemic regions in the world since May 2022. DNA replication of mpox is performed by DNA polymerase machinery F8-A22-E4, which is known as a great drug ...Mpox virus has wildly spread over 108 non-endemic regions in the world since May 2022. DNA replication of mpox is performed by DNA polymerase machinery F8-A22-E4, which is known as a great drug target. Brincidofovir and cidofovir are reported to have broad-spectrum antiviral activity against poxviruses, including mpox virus in animal models. However, the molecular mechanism is not understood. Here we report cryogenic electron microscopy structures of mpox viral F8-A22-E4 in complex with a DNA duplex, or dCTP and the DNA duplex, or cidofovir diphosphate and the DNA duplex at resolution of 3.22, 2.98 and 2.79 Å, respectively. Our structural work and DNA replication inhibition assays reveal that cidofovir diphosphate is located at the dCTP binding position with a different conformation to compete with dCTP to incorporate into the DNA and inhibit DNA synthesis. Conformation of both F8-A22-E4 and DNA is changed from the pre-dNTP binding state to DNA synthesizing state after dCTP or cidofovir diphosphate is bound, suggesting a coupling mechanism. This work provides the structural basis of DNA synthesis inhibition by brincidofovir and cidofovir, providing a rational strategy for new therapeutical development for mpox virus and other pox viruses. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j8f.cif.gz | 369.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j8f.ent.gz | 286.6 KB | Display | PDB format |
PDBx/mmJSON format | 8j8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j8f_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8j8f_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8j8f_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 8j8f_validation.cif.gz | 82.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/8j8f ftp://data.pdbj.org/pub/pdb/validation_reports/j8/8j8f | HTTPS FTP |
-Related structure data
Related structure data | 36068MC 8j86C 8j8gC C: citing same article (ref.) M: map data used to model this data |
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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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 120041.156 Da / Num. of mol.: 1 / Mutation: L108F, W411L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: F8L Production host: Insect expression vector pBlueBachsGCA1 (others) References: UniProt: Q5IXW8 |
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#2: Protein | Mass: 27883.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: E4R Production host: Insect expression vector pBlueBachsGCA1 (others) References: UniProt: Q5IXS4, uracil-DNA glycosylase |
#3: Protein | Mass: 49203.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: A22R Production host: Insect expression vector pBlueBachsGCA1 (others) References: UniProt: Q5IXP2 |
-DNA chain , 2 types, 2 molecules PT
#4: DNA chain | Mass: 7438.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
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#5: DNA chain | Mass: 11605.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
-Non-polymers , 2 types, 4 molecules
#6: Chemical | ChemComp-DCP / |
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#7: Chemical |
-Details
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 |
-Sample preparation
Component | Name: Monkeypox virus replication holoenzyme F8-A22-E4 in complex with a DNA duplex and dCTP Type: COMPLEX / Details: F8-A22-E4 in complex with a DNA duplex and dCTP / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 191 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Monkeypox virus |
Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM |
Buffer solution | pH: 7 Details: 25 mM MOPS, pH 7.0, 200 mM NaCl, 5% (w/v) glycerol, 1 mM TCEP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: F8-A22-E4 in complex with a DNA duplex and dCTP |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
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 |
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Image processing | Details: The selected movies are corrected with motion correct | ||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Details: 15,938,666 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1057305 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Refine LS restraints |
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