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- PDB-9zgf: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA -

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Basic information

Entry
Database: PDB / ID: 9zgf
TitleThe complex of HSV-1 proteins UL9 and ICP8 with forked DNA
Components
  • DNA (31-MER)
  • DNA (40-MER)
  • Major DNA-binding protein
  • Replication origin-binding protein
KeywordsREPLICATION/DNA / DNA replication / protein-DNA complex / REPLICATION-DNA complex
Function / homology
Function and homology information


nuclear viral factory / bidirectional double-stranded viral DNA replication / DNA replication origin binding / single-stranded DNA binding / DNA replication / host cell nucleus / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Replication origin-binding protein / Origin of replication binding protein / Viral ssDNA-binding protein / DBP-like superfamily / Viral ssDNA binding protein, head domain / ssDNA binding protein / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Major DNA-binding protein / Replication origin-binding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBaranovskiy, A.G. / Morstadt, L.M. / Romero, E.E. / Babayeva, N.D. / Tahirov, T.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152032 United States
CitationJournal: To Be Published
Title: Structural basis for unwinding the origins of HSV-1 genome by cooperative action of viral proteins UL9 and ICP8
Authors: Baranovskiy, A.G. / Morstadt, L.M. / Romero, E.E. / Babayeva, N.D. / Tahirov, T.H.
History
DepositionDec 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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: Major DNA-binding protein
C: Replication origin-binding protein
D: DNA (40-MER)
E: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,2357
Polymers244,6224
Non-polymers6133
Water00
1


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

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Major DNA-binding protein


Mass: 128486.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: DBP, ICP8, UL29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04296
#2: Protein Replication origin-binding protein / OBP / OriBP


Mass: 94371.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10193

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DNA chain , 2 types, 2 molecules DE

#3: DNA chain DNA (40-MER)


Mass: 12184.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human alphaherpesvirus 1 strain 17
#4: DNA chain DNA (31-MER)


Mass: 9579.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human alphaherpesvirus 1 strain 17

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: 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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 411805 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315872
ELECTRON MICROSCOPYf_angle_d0.49121826
ELECTRON MICROSCOPYf_dihedral_angle_d18.4422753
ELECTRON MICROSCOPYf_chiral_restr0.0392461
ELECTRON MICROSCOPYf_plane_restr0.0042626

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