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- EMDB-38396: The Cryo-EM structure of MPXV E5 C-terminal in complex with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-38396
TitleThe Cryo-EM structure of MPXV E5 C-terminal in complex with DNA
Map data
Sample
  • Virus: Monkeypox virus
    • DNA: DNA (70-MER)
    • Protein or peptide: Monkeypox virus E5
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordshelicase / REPLICATION
Function / homology
Function and homology information


helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / hydrolase activity / ATP binding
Similarity search - Function
DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncoating factor OPG117
Similarity search - Component
Biological speciesMonkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsZhang W / Liu Y / Gao H / Gan J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2024
Title: Structural and functional insights into the helicase protein E5 of Mpox virus.
Authors: Gan J / Zhang W
History
DepositionDec 20, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38396.png

Downloads & links

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Map

FileDownload / File: emd_38396.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.081 Å
Density
Contour LevelBy AUTHOR: 0.733
Minimum - Maximum-3.637654 - 8.139911
Average (Standard dev.)-0.0020091012 (±0.15927336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38396_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38396_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monkeypox virus

EntireName: Monkeypox virus
Components
  • Virus: Monkeypox virus
    • DNA: DNA (70-MER)
    • Protein or peptide: Monkeypox virus E5
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Monkeypox virus

SupramoleculeName: Monkeypox virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 10244 / Sci species name: Monkeypox virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: DNA (70-MER)

MacromoleculeName: DNA (70-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 21.440668 KDa
SequenceString: (DA)(DA)(DC)(DG)(DA)(DG)(DT)(DC)(DA)(DA) (DG)(DC)(DG)(DC)(DA)(DT)(DC)(DC)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT) ...String:
(DA)(DA)(DC)(DG)(DA)(DG)(DT)(DC)(DA)(DA) (DG)(DC)(DG)(DC)(DA)(DT)(DC)(DC)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DC)(DG)(DG)(DG)(DA)(DT)(DG)(DC) (DG)(DC) (DT)(DT)(DG)(DA)(DC)(DT)(DC) (DG)(DT)(DT)

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Macromolecule #2: Monkeypox virus E5

MacromoleculeName: Monkeypox virus E5 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 53.282012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GNKLFNIAQR ILDTNSVLLT ERGDHIVWIN NSWKFNSEEP LITKLILSIR HQLPKEYSSE LLCPRKRKTV EANIRDMLVD SVETDTYPD KLPFKNGVLD LVDGMFYSGD DAKKYTCTVS TGFKFDDTKF VEDSPEMEEL MNIINDIQPL TDENKKNREL Y EKTLSSCL ...String:
GNKLFNIAQR ILDTNSVLLT ERGDHIVWIN NSWKFNSEEP LITKLILSIR HQLPKEYSSE LLCPRKRKTV EANIRDMLVD SVETDTYPD KLPFKNGVLD LVDGMFYSGD DAKKYTCTVS TGFKFDDTKF VEDSPEMEEL MNIINDIQPL TDENKKNREL Y EKTLSSCL CGATKGCLTF FFGETATGKS TTKRLLKSAI GDLFVETGQT ILTDVLDKGP NPFIANMHLK RSVFCSELPD FA CSGSKKI RSDNIKKLTE PCVIGRPCFS NKINNRNHAT IIIDTNYKPV FDRIDNALMR RIAVVRFRTH FSQPSGREAA ENN DAYDKV KLLDEGLDGK IQNNRYRFAF LYLLVKWYKK YHIPIMKLYP TPEEIPDFAF YLKIGTLLVS SSVKHIPLMT DLSK KGYIL YDNVVTLPLT TFQQKISKYF NSRLFGHDIE SFINRHKKFA NVSDEYLQYI FIEDISSP

UniProtKB: Uncoating factor OPG117

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 3 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247898
FSC plot (resolution estimation)

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