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- PDB-9ja3: Herpes simplex virus type 1 polymerase machinery in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9ja3
TitleHerpes simplex virus type 1 polymerase machinery in complex with duplex DNA, acyclovir triphosphate and calcium ions
Components
  • DNA (27-MER)
  • DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
  • DNA polymerase
  • DNA polymerase processivity factor
KeywordsREPLICATION / Herpes simplex virus type 1 / HSV-1 / UL30 / UL42 / DNA replication holoenzyme / DNA replication machinery / acyclovir triphosphate / DNA / Calcium
Function / homology
Function and homology information


DNA polymerase complex / bidirectional double-stranded viral DNA replication / exonuclease activity / DNA polymerase processivity factor activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding ...DNA polymerase complex / bidirectional double-stranded viral DNA replication / exonuclease activity / DNA polymerase processivity factor activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B ...DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
ACYCLOVIR TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase / DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsWu, Y.Q. / Chen, X.L. / Jiang, Z.Y. / Li, D.Y. / Zhang, Z.Y. / Dong, C.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32250710142 China
CitationJournal: To Be Published
Title: Structural basis of herpes simplex type 1 virus DNA polymerase holoenzyme in DNA replication and acyclovir inhibition and proof-reading
Authors: Wu, Y.Q. / Chen, X.L. / Jiang, Z.Y. / Li, D.Y. / Zhang, Z.Y. / Dong, C.J.
History
DepositionAug 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
B: DNA polymerase processivity factor
T: DNA (27-MER)
P: DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,9008
Polymers206,3154
Non-polymers5854
Water00
1


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

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein DNA polymerase


Mass: 136683.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Gene: UL30
Production host: Insect expression vector pBlueBacmsGCA1 (others)
References: UniProt: G8HBE4, DNA-directed DNA polymerase
#2: Protein DNA polymerase processivity factor / DNA-binding protein UL42 / Polymerase accessory protein / PAP


Mass: 54288.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Gene: UL42
Production host: Insect expression vector pBlueBacmsGCA1His (others)
References: UniProt: P10226

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DNA chain , 2 types, 2 molecules TP

#3: DNA chain DNA (27-MER)


Mass: 8421.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')


Mass: 6921.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-AVP / ACYCLOVIR TRIPHOSPHATE


Mass: 465.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N5O12P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

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: Herpes simplex virus type 1 DNA replication machinery in complex DNA duplex and dGTP
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Source (recombinant)Organism: Insect expression vector pBlueBacmsGCA1His (others)
Buffer solutionpH: 7.2
Details: 25 mM MOPS, pH 7.2, 150mM NaCl, 5% glycerol, 1mM tris(2-carboxyethyl) phosphine (TCEP)
SpecimenConc.: 1.4 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 678158 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211845
ELECTRON MICROSCOPYf_angle_d0.48116292
ELECTRON MICROSCOPYf_dihedral_angle_d17.2411965
ELECTRON MICROSCOPYf_chiral_restr0.0411847
ELECTRON MICROSCOPYf_plane_restr0.0031936

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