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- PDB-8ww8: Structure of Apo-Form AsfvPrimPol Hexamer -

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Basic information

Entry
Database: PDB / ID: 8ww8
TitleStructure of Apo-Form AsfvPrimPol Hexamer
ComponentsPutative primase C962R
KeywordsDNA BINDING PROTEIN / VIRAL PROTEIN
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides / helicase activity / DNA replication
Similarity search - Function
Primase, C-terminal 2 / Primase C terminal 2 (PriCT-2) / : / 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
Putative primase C962R
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsShi, T.H. / Guo, Y.Y. / Yan, R.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of ADP-Form AsfvPrimPol Hexamer
Authors: Shi, T.H. / Guo, Y.Y. / Yan, R.H.
History
DepositionOct 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative primase C962R
B: Putative primase C962R
C: Putative primase C962R
D: Putative primase C962R
E: Putative primase C962R
F: Putative primase C962R


Theoretical massNumber of molelcules
Total (without water)676,3296
Polymers676,3296
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative primase C962R


Mass: 112721.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: C962R CDS / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A2X0TKI6
Has protein modificationN

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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: C962R Apo hexamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: African swine fever virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 7.5
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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33986 / Symmetry type: POINT

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