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- PDB-8iqi: Structure of Full-Length AsfvPrimPol in Complex-Form -

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Basic information

Entry
Database: PDB / ID: 8iqi
TitleStructure of Full-Length AsfvPrimPol in Complex-Form
Components
  • DNA (32-MER)
  • Putative primase C962R
KeywordsDNA BINDING PROTEIN / polymerase / primase / PrimPol / Helicase
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides / helicase activity / DNA replication / ATP binding / metal ion binding
Similarity search - Function
Primase, C-terminal 2 / Primase C terminal 2 (PriCT-2) / Domain of unknown function DUF5906 / Family of unknown function (DUF5906) / 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) / Putative primase C962R
Similarity search - Component
Biological speciesAfrican swine fever virus BA71V
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsShao, Z.W. / Su, S.C. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structures and implications of the C962R protein of African swine fever virus.
Authors: Zhiwei Shao / Shichen Su / Jie Yang / Weizhen Zhang / Yanqing Gao / Xin Zhao / Yixi Zhang / Qiyuan Shao / Chulei Cao / Huili Li / Hehua Liu / Jinru Zhang / Jinzhong Lin / Jinbiao Ma / Jianhua Gan /
Abstract: African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. Although it has been extensively studied in the past, no vaccine or other useful treatment against ASFV is ...African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. Although it has been extensively studied in the past, no vaccine or other useful treatment against ASFV is available. The genome of ASFV encodes more than 170 proteins, but the structures and functions for the majority of the proteins remain elusive, which hindered our understanding on the life cycle of ASFV and the development of ASFV-specific inhibitors. Here, we report the structural and biochemical studies of the highly conserved C962R protein of ASFV, showing that C962R is a multidomain protein. The N-terminal AEP domain is responsible for the DNA polymerization activity, whereas the DNA unwinding activity is catalyzed by the central SF3 helicase domain. The middle PriCT2 and D5_N domains and the C-terminal Tail domain all contribute to the DNA unwinding activity of C962R. C962R preferentially works on forked DNA, and likely functions in Base-excision repair (BER) or other repair pathway in ASFV. Although it is not essential for the replication of ASFV, C962R can serve as a model and provide mechanistic insight into the replicative primase proteins from many other species, such as nitratiruptor phage NrS-1, vaccinia virus (VACV) and other viruses.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)683,06117
Polymers679,9277
Non-polymers3,13410
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Putative primase C962R


Mass: 111706.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Gene: BA71V-C962R / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C5B022
#2: DNA chain DNA (32-MER)


Mass: 9689.213 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Full-Length AsfvPrimPol in complex with DNA and AMPPNPCOMPLEXASFV ORF C962R#1-#20MULTIPLE SOURCES
2Full-Length AsfvPrimPolCOMPLEX#11RECOMBINANT
3DNACOMPLEX#21SYNTHETIC
Molecular weightValue: 0.66 MDa / Experimental value: YES
Source (natural)Organism: African swine fever virus BA71V
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 589492 / Num. of class averages: 5 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00246622
ELECTRON MICROSCOPYf_angle_d0.4663274
ELECTRON MICROSCOPYf_dihedral_angle_d5.956114
ELECTRON MICROSCOPYf_chiral_restr0.0396800
ELECTRON MICROSCOPYf_plane_restr0.0047983

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