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- EMDB-65113: Cryo-EM structure of UL9-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65113
TitleCryo-EM structure of UL9-DNA complex
Map data
Sample
  • Complex: HSV-1 UL9-DNA complex
    • Protein or peptide: Replication origin-binding protein
    • DNA: 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: 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')
KeywordsHelicase ATPase DNA-binding Dimerization / VIRAL PROTEIN/DNA / 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
Replication origin-binding protein
Similarity search - Component
Biological speciesHuman herpesvirus 1 (strain 17) / Human alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMa J / Zhang X / Huang C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Virol / Year: 2026
Title: Structure and mechanism of the HSV-1 origin-binding protein UL9.
Authors: Cuiqing Huang / Haiqiang Wu / Jinmiao Song / Xinzheng Zhang / Jun Ma /
Abstract: The herpesvirus DNA replication machinery comprises a battery of viral enzymes that orchestrate viral genome synthesis. In herpes simplex virus type 1 (HSV-1), the machinery consists of seven ...The herpesvirus DNA replication machinery comprises a battery of viral enzymes that orchestrate viral genome synthesis. In herpes simplex virus type 1 (HSV-1), the machinery consists of seven essential components, including the origin-binding protein UL9, the single-stranded DNA (ssDNA)-binding protein ICP8, the heterodimeric DNA polymerase complex UL30-UL42, and the heterotrimeric helicase-primase complex UL5-UL8-UL52. UL9, a superfamily 2 (SF2) helicase, functions as a dimer that specifically recognizes replication origins and unwinds duplex DNA to initiate replication. Furthermore, UL9 recruits the replication machinery through interactions with viral components and engages cellular proteins that regulate its function. However, the molecular mechanisms underlying the multifunctionality of UL9 remain incompletely understood due to the lack of structural information. Here, we present cryo-electron microscopy structures of UL9 in both apo and DNA-bound states. Together with biochemical and enzymatic assays, we elucidate the molecular basis of UL9 dimerization, origin recognition and allosteric regulation by ICP8.IMPORTANCEHerpes simplex virus 1 (HSV-1) is a widespread virus that causes lifelong infections, leading to periodic outbreaks ranging from common cold sores to life-threatening encephalitis, and no current treatment can eradicate the dormant virus. To multiply, HSV-1 relies on a protein-based molecular machine to replicate its genome, where the unwinding of double-stranded DNA at specific replication origins is coordinated by the viral origin-binding protein UL9. Here, we present the high-resolution structures of UL9, both alone and bound to DNA, revealing how it forms a stable homodimer to grab onto the origin. Combined with precise biochemical experiments, we further show how UL9 collaborates with another viral helper protein, ICP8, to unwind DNA efficiently. These discoveries solve a long-standing puzzle in herpesvirus biology and offer a vital structural blueprint for designing new antiviral drugs that can block viral replication at its very earliest stage.
History
DepositionJun 20, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65113.png

Downloads & links

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Map

FileDownload / File: emd_65113.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 240 pix.
= 196.8 Å		0.82 Å/pix.
x 240 pix.
= 196.8 Å		0.82 Å/pix.
x 240 pix.
= 196.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.08834085 - 0.14615601
Average (Standard dev.)0.00036059538 (±0.004108185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 196.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65113_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_65113_half_map_2.map
Projections & Slices
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Sample components

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Entire : HSV-1 UL9-DNA complex

EntireName: HSV-1 UL9-DNA complex
Components
  • Complex: HSV-1 UL9-DNA complex
    • Protein or peptide: Replication origin-binding protein
    • DNA: 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: 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')

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Supramolecule #1: HSV-1 UL9-DNA complex

SupramoleculeName: HSV-1 UL9-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Molecular weightTheoretical: 190 kDa/nm

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Macromolecule #1: Replication origin-binding protein

MacromoleculeName: Replication origin-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 97.331781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK PFVGGAESGD PLGAGRPIGD DECEQYTSSV SLARMLYGGD LAEWVPRVHP KTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTTA LIRWLREAIH SPDTSVLVVS CRRSFTQTLA TRFAESGLVD F VTYFSSTN ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK PFVGGAESGD PLGAGRPIGD DECEQYTSSV SLARMLYGGD LAEWVPRVHP KTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTTA LIRWLREAIH SPDTSVLVVS CRRSFTQTLA TRFAESGLVD F VTYFSSTN YIMNDRPFHR LIVQVESLHR VGPNLLNNYD VLVLDEVMST LGQLYSPTMQ QLGRVDALML RLLRICPRII AM DATANAQ LVDFLCGLRG EKNVHVVVGE YAMPGFSARR CLFLPRLGTE LLQAALRPPG PPSGPSPDAS PEARGATFFG ELE ARLGGG DNICIFSSTV SFAEIVARFC RQFTDRVLLL HSLTPLGDVT TWGQYRVVIY TTVVTVGLSF DPLHFDGMFA YVKP MNYGP DMVSVYQSLG RVRTLRKGEL LIYMDGSGAR SEPVFTPMLL NHVVSSCGQW PAQFSQVTNL LCRRFKGRCD ASACD TSLG RGSRIYNKFR YKHYFERCTL ACLSDSLNIL HMLLTLNCIR VRFWGHDDTL TPKDFCLFLR GVHFDALRAQ RDLREL RCR DPEASLPAQA AETEEVGLFV EKYLRSDVAP AEIVALMRNL NSLMGRTRFI YLALLEACLR VPMATRSSAI FRRIYDH YA TGVIPTINVT GELELVALPP TLNVTPVWEL LCLCSTMAAR LHWDSAAGGS GRTFGPDDVL DLLTPHYDRY MQLVFELG H CNVTDGLLLS EEAVKRVADA LSGCPPRGSV SETDHAVALF KIIWGELFGV QMAKSTQTFP GAGRVKNLTK QTIVGLLDA HHIDHSACRT HRQLYALLMA HKREFAGARF KLRVPAWGRC LRTHSSSANP NADIILEAAL SELPTEAWPM MQGAVNFSTL

UniProtKB: Replication origin-binding protein

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Macromolecule #2: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP...

MacromoleculeName: 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')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 6.97651 KDa
SequenceString:
(DA)(DG)(DC)(DG)(DT)(DT)(DC)(DG)(DC)(DA) (DC)(DT)(DT)(DC)(DG)(DT)(DC)(DC)(DC)(DA) (DA)(DT)(DA)

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Macromolecule #3: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP...

MacromoleculeName: 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')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 7.145621 KDa
SequenceString:
(DT)(DA)(DT)(DT)(DG)(DG)(DG)(DA)(DC)(DG) (DA)(DA)(DG)(DT)(DG)(DC)(DG)(DA)(DA)(DC) (DG)(DC)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 110702
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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