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- PDB-9ivf: Structure of Full-Length AsfvPrimPol with polyT DNA -

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Basic information

Entry
Database: PDB / ID: 9ivf
TitleStructure of Full-Length AsfvPrimPol with polyT DNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Putative primase C962R
KeywordsDNA BINDING PROTEIN / Primase/helicase/DNA-binding
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) / C962R protein N-terminal AEP domain / : / 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 / Putative primase C962R
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXu, K.E. / Chen, Y.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Full-Length AsfvPrimPol with polyT DNA
Authors: Xu, K.E. / Chen, Y.T.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 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
G: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)674,31913
Polymers671,2827
Non-polymers3,0376
Water00
1


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

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Components

#1: Protein
Putative primase C962R


Mass: 111482.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: C962R CDS, C962R, ASFV-Georgia_4-095 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2X0TKI6
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2388.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
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: African swine fever virus / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: African swine fever virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: PRION
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 253584 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00533157
ELECTRON MICROSCOPYf_angle_d0.86544989
ELECTRON MICROSCOPYf_dihedral_angle_d8.3594332
ELECTRON MICROSCOPYf_chiral_restr0.0534709
ELECTRON MICROSCOPYf_plane_restr0.0075645

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