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- PDB-8xj8: The Cryo-EM structure of MPXV E5 C-terminal in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 8xj8
TitleThe Cryo-EM structure of MPXV E5 C-terminal in complex with DNA
Components
  • DNA (70-MER)
  • Monkeypox virus E5
KeywordsREPLICATION / helicase
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Uncoating factor OPG117
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsZhang, W. / Liu, Y. / Gao, H. / Gan, J.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA (70-MER)
A: Monkeypox virus E5
B: Monkeypox virus E5
C: Monkeypox virus E5
D: Monkeypox virus E5
E: Monkeypox virus E5
F: Monkeypox virus E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,72413
Polymers341,1337
Non-polymers1,5926
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain DNA (70-MER)


Mass: 21440.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Monkeypox virus
#2: Protein
Monkeypox virus E5


Mass: 53282.012 Da / Num. of mol.: 6 / Fragment: C-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG117, MPXVgp100 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7H0DN89, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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 / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: YES / Isolate: SPECIES / Type: VIRION
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.1_4122: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247898 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216253
ELECTRON MICROSCOPYf_angle_d0.55322003
ELECTRON MICROSCOPYf_dihedral_angle_d9.2862193
ELECTRON MICROSCOPYf_chiral_restr0.0412491
ELECTRON MICROSCOPYf_plane_restr0.0042765

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