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- EMDB-37721: Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with... -

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Entry
Database: EMDB / ID: EMD-37721
TitleStructure of monkeypox virus polymerase complex F8-A22-E4-H5 with exogenous DNA bearing one abasic site, the region of H5 optimized
Map data
Sample
  • Complex: F8-A22-E4-H5 with exogenous DNA bearing one abasic site
KeywordsViral DNA replication / monkeypox virus / polymerase / H5 / VIRAL PROTEIN
Biological speciesMonkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang X / Li N / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
Citation
Journal: Mol Cell / Year: 2023
Title: Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5.
Authors: Xiaohan Wang / Liangwen Ma / Ningning Li / Ning Gao /
Abstract: The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. ...The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. However, the molecular roles of these viral factors remain unclear. Here, we characterize the structures of F8-A22-E4 and F8-A22-E4-H5 complexes in the presence of different primer-template DNA substrates. E4 is located upstream of F8 on the template single-stranded DNA (ssDNA) and is catalytically active, highlighting a functional coupling between DNA base-excision repair and DNA synthesis. Moreover, H5, in the form of tetramer, binds to the double-stranded DNA (dsDNA) region downstream of F8 in a similar position as PCNA (proliferating cell nuclear antigen) does in eukaryotic polymerase complexes. Omission of H5 or disruption of its DNA interaction showed a reduced synthesis of full-length DNA products. These structures provide snapshots for the working cycle of the polymerase and generate insights into the mechanisms of these essential factors in viral DNA replication.
#1: Journal: Mol.Cell / Year: 2023
Title: Structural insights into the assembly and mechanism of monkeypox virus DNA polymerase complex F8-A22-E4-H5
Authors: Wang X / Ma L / Li N / Gao N
History
DepositionOct 10, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37721.png

Downloads & links

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Map

FileDownload / File: emd_37721.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.75622547 - 1.1825544
Average (Standard dev.)0.00023871077 (±0.019123875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37721_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Half map: #2

Fileemd_37721_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : F8-A22-E4-H5 with exogenous DNA bearing one abasic site

EntireName: F8-A22-E4-H5 with exogenous DNA bearing one abasic site
Components
  • Complex: F8-A22-E4-H5 with exogenous DNA bearing one abasic site

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Supramolecule #1: F8-A22-E4-H5 with exogenous DNA bearing one abasic site

SupramoleculeName: F8-A22-E4-H5 with exogenous DNA bearing one abasic site
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Monkeypox virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139000

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