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- PDB-9vjh: Cryo-EM structure of UL9-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9vjh
TitleCryo-EM structure of UL9-DNA complex
Components
  • DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')
  • Replication origin-binding protein
KeywordsVIRAL PROTEIN/DNA / Helicase ATPase DNA-binding Dimerization / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA replication origin binding / DNA replication / host cell nucleus / ATP binding
Similarity search - Function
Replication origin-binding protein / Origin of replication 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
DNA / DNA (> 10) / Replication origin-binding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMa, J. / Zhang, X. / Huang, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of UL9-DNA complex
Authors: Ma, J. / Zhang, X. / Huang, C.
History
DepositionJun 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 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

Downloads & links

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Assembly

Deposited unit
A: Replication origin-binding protein
B: Replication origin-binding protein
C: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
E: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
D: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')
F: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)222,9086
Polymers222,9086
Non-polymers00
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 Replication origin-binding protein / OBP / OriBP


Mass: 97331.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10193
#2: DNA chain DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')


Mass: 6976.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human alphaherpesvirus 1 strain 17
#3: DNA chain DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')


Mass: 7145.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human alphaherpesvirus 1 strain 17
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: HSV-1 UL9-DNA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 190 kDa/nm / Experimental value: NO
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487model refinement
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110702 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214452
ELECTRON MICROSCOPYf_angle_d0.51120010
ELECTRON MICROSCOPYf_dihedral_angle_d18.9882606
ELECTRON MICROSCOPYf_chiral_restr0.0352282
ELECTRON MICROSCOPYf_plane_restr0.0042238

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