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- PDB-8ww6: Structure of ATP-rs-Form AsfvPrimPol Hexamer -

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Basic information

Entry
Database: PDB / ID: 8ww6
TitleStructure of ATP-rs-Form AsfvPrimPol Hexamer
Components
  • DNA (25-MER)
  • DNA (5'-D(P*AP*AP*AP*A)-3')
  • Putative primase C962R
KeywordsDNA BINDING PROTEIN/DNA / VIRAL PROTEIN / DNA BINDING PROTEIN-DNA COMPLEX
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Putative primase C962R
Similarity search - Component
Biological speciesAfrican swine fever virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 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
H: DNA (25-MER)
I: DNA (5'-D(P*AP*AP*AP*A)-3')
B: Putative primase C962R
A: Putative primase C962R
C: Putative primase C962R
D: Putative primase C962R
E: Putative primase C962R
F: Putative primase C962R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)688,38220
Polymers685,0978
Non-polymers3,28512
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: DNA chain DNA (25-MER)


Mass: 7559.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*AP*AP*AP*A)-3')


Mass: 1207.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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 ATP-rs-Form hexamer / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: African swine fever virus
Source (recombinant)Organism: Homo sapiens (human)
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: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38908 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334364
ELECTRON MICROSCOPYf_angle_d0.59646718
ELECTRON MICROSCOPYf_dihedral_angle_d12.4514640
ELECTRON MICROSCOPYf_chiral_restr0.0414914
ELECTRON MICROSCOPYf_plane_restr0.0045800

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