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- EMDB-34885: F8-A22-E4 complex in hexameric form local map -

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Basic information

Entry
Database: EMDB / ID: EMD-34885
TitleF8-A22-E4 complex in hexameric form local map
Map data
Sample
  • Complex: F8-A22-E4 complex of MPXV in hexameric form
    • Complex: DNA polymerase processivity factor component A20
    • Complex: E4R
    • Complex: DNA polymerase
KeywordsMPXV / complex / RECOMBINATION / REPLICATION
Biological speciesMonkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi YN / Shen YP / Hu ZW / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis for the assembly of the DNA polymerase holoenzyme from a monkeypox virus variant.
Authors: Yaning Li / Yaping Shen / Ziwei Hu / Renhong Yan /
Abstract: The ongoing global pandemic caused by a variant of the monkeypox (or mpox) virus (MPXV) has prompted widespread concern. The MPXV DNA polymerase holoenzyme, consisting of F8, A22, and E4, is vital ...The ongoing global pandemic caused by a variant of the monkeypox (or mpox) virus (MPXV) has prompted widespread concern. The MPXV DNA polymerase holoenzyme, consisting of F8, A22, and E4, is vital for replicating the viral genome and represents a crucial target for the development of antiviral drugs. However, the assembly and working mechanism for the DNA polymerase holoenzyme of MPXV remains elusive. Here, we present the cryo-electron microscopy (cryo-EM) structure of the DNA polymerase holoenzyme at an overall resolution of 3.5 Å. Unexpectedly, the holoenzyme is assembled as a dimer of heterotrimers, of which the extra interface between the thumb domain of F8 and A22 shows a clash between A22 and substrate DNA, suggesting an autoinhibition state. Addition of exogenous double-stranded DNA shifts the hexamer into trimer exposing DNA binding sites, potentially representing a more active state. Our findings provide crucial steps toward developing targeted antiviral therapies for MPXV and related viruses.
History
DepositionDec 2, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34885.png

Downloads & links

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Map

FileDownload / File: emd_34885.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 288 pix.
= 315.36 Å		1.1 Å/pix.
x 288 pix.
= 315.36 Å		1.1 Å/pix.
x 288 pix.
= 315.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.055695176 - 0.09823421
Average (Standard dev.)0.00007658405 (±0.0018256113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 315.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34885_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34885_half_map_2.map
Projections & Slices
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Sample components

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Entire : F8-A22-E4 complex of MPXV in hexameric form

EntireName: F8-A22-E4 complex of MPXV in hexameric form
Components
  • Complex: F8-A22-E4 complex of MPXV in hexameric form
    • Complex: DNA polymerase processivity factor component A20
    • Complex: E4R
    • Complex: DNA polymerase

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Supramolecule #1: F8-A22-E4 complex of MPXV in hexameric form

SupramoleculeName: F8-A22-E4 complex of MPXV in hexameric form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Monkeypox virus

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Supramolecule #2: DNA polymerase processivity factor component A20

SupramoleculeName: DNA polymerase processivity factor component A20 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Monkeypox virus

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Supramolecule #3: E4R

SupramoleculeName: E4R / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Monkeypox virus

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Supramolecule #4: DNA polymerase

SupramoleculeName: DNA polymerase / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 383777
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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