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- PDB-8hdz: Monkeypox virus DNA replication holoenzyme F8, A22 and E4 complex... -

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Basic information

Entry
Database: PDB / ID: 8hdz
TitleMonkeypox virus DNA replication holoenzyme F8, A22 and E4 complex in an apo form
Components
  • A22 DNA replication processivity factor
  • E4 uracil-DNA glycosylase
  • F8 DNA polymerase
KeywordsVIRAL PROTEIN / DNA replication machinery / F8 / A22 / E4 / 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 / DNA-templated DNA replication / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase 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 polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / 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 polymerase processivity factor / Uracil-DNA glycosylase / DNA polymerase
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsXu, Y. / Wu, Y. / Zhang, Y. / Fan, R. / Yang, Y. / Li, D. / Yang, B. / Zhang, Z. / Dong, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32250710142 China
CitationJournal: Cell Res / Year: 2023
Title: Cryo-EM structures of human monkeypox viral replication complexes with and without DNA duplex.
Authors: Yunxia Xu / Yaqi Wu / Yuanyuan Zhang / Ruixin Fan / Yaxue Yang / Danyang Li / Shimin Zhu / Biao Yang / Zhengyu Zhang / Changjiang Dong /
History
DepositionNov 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F8 DNA polymerase
C: A22 DNA replication processivity factor
B: E4 uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)197,1293
Polymers197,1293
Non-polymers00
Water00
1


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

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Components

#1: Protein F8 DNA polymerase


Mass: 120041.156 Da / Num. of mol.: 1 / Mutation: L108F, M411L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: F8L / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5IXW8, DNA-directed DNA polymerase
#2: Protein A22 DNA replication 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 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5IXP2
#3: Protein E4 uracil-DNA glycosylase


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: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5IXS4, uracil-DNA glycosylase

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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 replication holoenzyme F8-A22-E4 complex
Type: COMPLEX / Details: F8-A22-E4 complex / Entity ID: #1, #3, #2 / Source: RECOMBINANT
Molecular weightValue: 191 kDa/nm / Experimental value: NO
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 8
Details: 25mM HEPES pH 8.0, 300mM NaCl, 5% (w/v) glycerol, and 1 mM TCEP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This is a complex of F8-A22-E4
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU9.03image acquisition
4cryoSPARCCTF correction
12cryoSPARCclassification
13cryoSPARC3D reconstruction
Image processingDetails: The selected movies are corrected with motion correct
CTF correctionType: NONE
Particle selectionDetails: 19,555,002
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 632071 / Num. of class averages: 4 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212120
ELECTRON MICROSCOPYf_angle_d0.42616387
ELECTRON MICROSCOPYf_dihedral_angle_d3.3821604
ELECTRON MICROSCOPYf_chiral_restr0.041817
ELECTRON MICROSCOPYf_plane_restr0.0032085

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