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- PDB-9leb: DNA polymerase holoenzyme -

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Basic information

Entry
Database: PDB / ID: 9leb
TitleDNA polymerase holoenzyme
Components
  • DNA (25-MER)
  • DNA (38-MER)
  • DNA polymerase
  • DNA polymerase processivity factor
  • Uracil-DNA glycosylase
KeywordsVIRAL PROTEIN/DNA / DNA replication holoenzyme / DNA molecule / MPXV / F8-A22-E4 complex / VIRAL PROTEIN-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 / hydrolase activity / 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
: / 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: 2.73 Å
AuthorsWang, N. / Li, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Development of 2a as a Potent Inhibitor of MPXV: Mechanistic and Structural Characterization
Authors: Wang, N. / Li, Y.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,2537
Polymers210,7285
Non-polymers5242
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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: 117057.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG071, POL, MPXVgp056 / Production host: Spodoptera (butterflies/moths)
References: UniProt: A0A7H0DN44, DNA-directed DNA polymerase
#2: Protein Uracil-DNA glycosylase


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
#3: Protein DNA polymerase processivity factor / DNA polymerase processivity factor component A20 / MPXV-COP-126 / MPXV-SL-126 / MPXV-WRAIR126 / ...DNA polymerase processivity factor component A20 / MPXV-COP-126 / MPXV-SL-126 / MPXV-WRAIR126 / MPXVgp132 / Viral DNA polymerase processivity factor


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: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Production host: Spodoptera (butterflies/moths)
#5: DNA chain DNA (38-MER)


Mass: 11677.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Production host: Spodoptera (butterflies/moths)

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-A1EKM / [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 500.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16FN2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / 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: Monkeypox virus / Type: VIRUS
Details: DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and 2f-TP
Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SUBSPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347619 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00714188
ELECTRON MICROSCOPYf_angle_d0.66319416
ELECTRON MICROSCOPYf_dihedral_angle_d14.9932190
ELECTRON MICROSCOPYf_chiral_restr0.0472203
ELECTRON MICROSCOPYf_plane_restr0.0052313

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