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- PDB-8hg1: The structure of MPXV polymerase holoenzyme in replicating state -

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Basic information

Entry
Database: PDB / ID: 8hg1
TitleThe structure of MPXV polymerase holoenzyme in replicating state
Components
  • DNA (25-MER)
  • DNA (38-MER)
  • DNA polymerase
  • DNA polymerase processivity factor component A20
  • E4R
KeywordsREPLICATION/DNA / MPXV / Polymerase / Replication / REPLICATION-DNA complex
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / viral DNA genome replication / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA repair / nucleotide binding / DNA binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / : ...DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / Chordopoxvirus A20R / Chordopoxvirus A20R protein / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like domain superfamily / : / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase / DNA polymerase processivity factor / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPeng, Q. / Xie, Y.F. / Kuai, L. / Wang, H. / Qi, J.X. / Gao, F. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2023
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
DepositionNov 13, 2022Deposition site: PDBJ / Processing site: PDBC
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Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
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Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
B: E4R
C: DNA polymerase processivity factor component A20
P: DNA (25-MER)
T: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,1177
Polymers213,6105
Non-polymers5062
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein DNA polymerase


Mass: 119939.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
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: Spodoptera (butterflies/moths)
References: UniProt: A0A2L0AR76, DNA-directed DNA polymerase
#2: Protein E4R / MPXV-COP-095 / MPXV-SL-095 / MPXV-WRAIR095 / MPXVgp101 / Uracil-DNA glycosylase / Uracil-DNA ...MPXV-COP-095 / MPXV-SL-095 / MPXV-WRAIR095 / MPXVgp101 / Uracil-DNA glycosylase / Uracil-DNA glycosylase DNA polymerase / Uracil-DNA glycosylase interacts with A20R / DNA polymerase processivity factor


Mass: 25107.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
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: Spodoptera (butterflies/moths) / References: UniProt: Q5IXS4, uracil-DNA glycosylase
#3: Protein DNA polymerase processivity factor component A20


Mass: 49203.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
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: Spodoptera (butterflies/moths) / References: UniProt: Q5IXP2

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DNA chain , 2 types, 2 molecules PT

#4: DNA chain DNA (25-MER)


Mass: 7681.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Monkeypox virus
#5: DNA chain DNA (38-MER)


Mass: 11677.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Monkeypox virus

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MPXV DNA polymerase holoenzyme / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43819 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414537
ELECTRON MICROSCOPYf_angle_d0.63819806
ELECTRON MICROSCOPYf_dihedral_angle_d14.8075508
ELECTRON MICROSCOPYf_chiral_restr0.0422193
ELECTRON MICROSCOPYf_plane_restr0.0052389

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