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Open data
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Basic information
Entry | Database: PDB / ID: 8hg1 | ||||||
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Title | The structure of MPXV polymerase holoenzyme in replicating state | ||||||
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![]() | REPLICATION/DNA / MPXV / ![]() ![]() | ||||||
Function / homology | ![]() viral DNA genome replication / uracil DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, Q. / Xie, Y.F. / Kuai, L. / Wang, H. / Qi, J.X. / Gao, F. / Shi, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of monkeypox virus DNA polymerase holoenzyme. Authors: Qi Peng / Yufeng Xie / Lu Kuai / Han Wang / Jianxun Qi / George F Gao / Yi Shi / ![]() Abstract: The World Health Organization declared mpox (or monkeypox) a public health emergency of international concern in July 2022, and prophylactic and therapeutic measures are in urgent need. The monkeypox ...The World Health Organization declared mpox (or monkeypox) a public health emergency of international concern in July 2022, and prophylactic and therapeutic measures are in urgent need. The monkeypox virus (MPXV) has its own DNA polymerase F8, together with the processive cofactors A22 and E4, constituting the polymerase holoenzyme for genome replication. Here, we determined the holoenzyme structure in complex with DNA using cryo-electron microscopy at the global resolution of ~2.8 angstroms. The holoenzyme possesses an architecture that suggests a "forward sliding clamp" processivity mechanism for viral DNA replication. MPXV polymerase has a DNA binding mode similar to that of other B-family DNA polymerases from different species. These findings reveal the mechanism of the MPXV genome replication and may guide the development of anti-poxvirus drugs. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 348.8 KB | Display | ![]() |
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PDB format | ![]() | 269.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34731MC 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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1 |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | ![]() Mass: 119939.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: POL, MPXV-M2940_FCT-055, MPXV-M2957_Lagos-055, MPXV-M3021_Delta-055, MPXV-M5320_M15_Bayelsa-048, MPXV-Singapore-055, MPXV-UK_P1-055, MPXV-UK_P2-055, MPXV-UK_P3-055, MPXV298464_038, PDLMKLCO_00060 Production host: ![]() ![]() References: UniProt: A0A2L0AR76, ![]() |
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#2: Protein | Mass: 25107.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: E4R, UNG, MPXV-CAM1990_02-093, MPXV-Congo_8-094, MPXV-COP-095, MPXV-GAB1988_001-094, MPXV-Ikubi-093, MPXV-M2940_FCT-099, MPXV-M2957_Lagos-099, MPXV-M3021_Delta-099, MPXV-M5320_M15_Bayelsa-092, ...Gene: E4R, UNG, MPXV-CAM1990_02-093, MPXV-Congo_8-094, MPXV-COP-095, MPXV-GAB1988_001-094, MPXV-Ikubi-093, MPXV-M2940_FCT-099, MPXV-M2957_Lagos-099, MPXV-M3021_Delta-099, MPXV-M5320_M15_Bayelsa-092, MPXV-Nig_SEV71_2_82-094, MPXV-PCH-096, MPXV-Singapore-099, MPXV-SL-095, MPXV-UK_P1-099, MPXV-UK_P2-099, MPXV-UK_P3-099, MPXV-USA2003_099_GR-099, MPXV-USA2003_206_DM-099, MPXV-USA2003_223_RS-099, MPXV-UTC-090, MPXV-W_Nigeria-094, MPXV-WRAIR095, MPXV297957_090, MPXV298464_081, MPXV_DRC_Yandongi_102, MPXV_LIB1970_184_106, MPXV_RCG2003_358_106, MPXV_SUD2005_01_102, MPXV_USA2003_039_106, MPXV_USA2003_044_106, MPXV_ZAI1979_005_106, MPXVgp101, PDLMKLCO_00104 Production host: ![]() ![]() ![]() |
#3: Protein | Mass: 49203.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: A22R, MPXV-COP-126, MPXV-M2940_FCT-131, MPXV-M2957_Lagos-131, MPXV-M3021_Delta-131, MPXV-M5320_M15_Bayelsa-124, MPXV-Nig_SEV71_2_82-126, MPXV-PCH-128, MPXV-Singapore-131, MPXV-SL-126, MPXV-UK_ ...Gene: A22R, MPXV-COP-126, MPXV-M2940_FCT-131, MPXV-M2957_Lagos-131, MPXV-M3021_Delta-131, MPXV-M5320_M15_Bayelsa-124, MPXV-Nig_SEV71_2_82-126, MPXV-PCH-128, MPXV-Singapore-131, MPXV-SL-126, MPXV-UK_P1-131, MPXV-UK_P2-131, MPXV-UK_P3-131, MPXV-USA2003_099_GR-131, MPXV-USA2003_206_DM-131, MPXV-USA2003_223_RS-131, MPXV-UTC-122, MPXV-W_Nigeria-126, MPXV-WRAIR126, MPXV297957_122, MPXV298464_113, MPXV_LIB1970_184_138, MPXV_USA2003_039_138, MPXV_USA2003_044_138, PDLMKLCO_00135 Production host: ![]() ![]() |
-DNA chain , 2 types, 2 molecules PT
#4: DNA chain | Mass: 7681.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#5: DNA chain | Mass: 11677.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/TTP.gif)
#6: Chemical | ChemComp-MG / |
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#7: Chemical | ChemComp-TTP / ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: MPXV DNA polymerase holoenzyme / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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![]() |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43819 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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