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- EMDB-52135: HSV-1 Origin Binding Protein in complex with double-stranded DNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52135
TitleHSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region
Map data
Sample
  • Complex: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region
    • Protein or peptide: Replication origin-binding protein
    • 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*TP*T)-3')
    • DNA: DNA (5'-D(P*AP*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
KeywordsDNA / Helicase / Complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA replication origin binding / helicase activity / 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 alphaherpesvirus 1 strain KOS / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsGustavsson E / Grunewald K / Elias P / Hallberg BM
Funding support Sweden, Germany, 2 items
OrganizationGrant numberCountry
Swedish Research Council2017-06702 Sweden
German Research Foundation (DFG)152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 FUGG Germany
CitationJournal: Nucleic Acids Res / Year: 2025
Title: The herpes simplex origin-binding protein: mechanisms for sequence-specific DNA binding and dimerization revealed by Cryo-EM.
Authors: Emil Gustavsson / Kay Grünewald / Per Elias / B Martin Hällberg /
Abstract: Herpes simplex viruses 1 and 2 (HSV-1,2) present growing treatment challenges due to increasing resistance to antivirals targeting viral DNA polymerase, particularly in immunocompromised individuals. ...Herpes simplex viruses 1 and 2 (HSV-1,2) present growing treatment challenges due to increasing resistance to antivirals targeting viral DNA polymerase, particularly in immunocompromised individuals. The HSV-1 origin-binding protein (OBP), an essential Superfamily 2 (SF2) DNA helicase encoded by the UL9 gene, is a promising alternative therapeutic target. Here, we present cryo-EM structures of OBP at up to 2.8 Å resolution in multiple conformational states, including complexes with the OriS recognition sequence and the non-hydrolyzable ATP analog ATPγS. The structures reveal an unexpected head-to-tail dimer stabilized by the C-terminal domain, where the conserved RVKNL motif mediates sequence-specific DNA recognition. The C-terminal domain extends into the partner monomer, suggesting a regulatory mechanism involving the single-stranded DNA-binding protein ICP8. We also resolve an OBP monomer bound to a DNA hairpin with a 3' single-stranded tail (mini-OriS*), and at lower resolution, a dimer-dimer assembly of two OBP dimers bound simultaneously to OriS or mini-OriS*. These structures uncover the molecular basis of HSV-1 origin recognition and unwinding, and identify multiple druggable interfaces, laying the groundwork for structure-based antiviral development targeting HSV-1 OBP.
History
DepositionNov 19, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52135.png

Downloads & links

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Map

FileDownload / File: emd_52135.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.33789626 - 0.77953094
Average (Standard dev.)0.00020880664 (±0.014145242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52135_msk_1.map
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Additional map: #1

Fileemd_52135_additional_1.map
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Half map: #1

Fileemd_52135_half_map_1.map
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Half map: #2

Fileemd_52135_half_map_2.map
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Sample components

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Entire : HSV-1 Origin Binding Protein in complex with double-stranded DNA ...

EntireName: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region
Components
  • Complex: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region
    • Protein or peptide: Replication origin-binding protein
    • 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*TP*T)-3')
    • DNA: DNA (5'-D(P*AP*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')

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Supramolecule #1: HSV-1 Origin Binding Protein in complex with double-stranded DNA ...

SupramoleculeName: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS

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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 KOS
Molecular weightTheoretical: 95.677102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKS AMPFVGGAES GDPLGAGRPI GDDECEQYTS SVSLARMLYG GDLAEWVPRV HPKTTIERQQ HGPVTFPNAS APTARCVTV VRAPMGSGKT TALIRWLREA IHSPDTSVLV VSCRRSFTQT LATRFAESGL VDFVTYFSST NYIMNDRPFH R LIVQVESL ...String:
MWSHPQFEKS AMPFVGGAES GDPLGAGRPI GDDECEQYTS SVSLARMLYG GDLAEWVPRV HPKTTIERQQ HGPVTFPNAS APTARCVTV VRAPMGSGKT TALIRWLREA IHSPDTSVLV VSCRRSFTQT LATRFAESGL VDFVTYFSST NYIMNDRPFH R LIVQVESL HRVGPNLLNN YDVLVLDEVM STLGQLYSPT MQQLGRVDAL MLRLLRTCPR IIAMDATANA QLVDFLCGLR GE KNVHVVV GEYAMPGFSA RRCLFLPRLG TELLQAALRP PGPPSGPSPD ASPDARGATF FGELEARLGG GDNICIFSST VSF AEIVAR FCRQFTDRVL LLHSLTPLGD VTTWGQYRVV IYTTVVTVGL SFDPLHFDGM FAYVKPMNYG PDMVSVYQSL GRVR TLRKG ELLIYMDGSG ARSEPVFTPM LLNHVVSSCG QWPAQFSQVT NLLCRRFKGR CDASACDTSL GRGSRIYNKF RYKHY FERC TLACLSDSLN ILHMLLTLNC IRVRFWGHDD TLTPKDFCLF LRGVHFDALR AQRDLRELRC RDPEASLPAQ AAETEE VGL FVEKYLRSDV APAEIVALMR NLNSLMGRTR FIYLALLEAC LRVPMATRSS AIFRRIYDHY ATGVIPTINV TGELELV AL PPTLNVTPVW ELLCLCSTMA ARLHWDSAAG GSGRTFGPDD VLDLLTPHYD RYMQLVFELG HCNVTDGLLL SEEAVKRV A DALSGCPPRG SVSETDHAVA LFKIIWGELF GVQMAKSTQT FPGAGRVKNL TKQTIVGLLD AHHIDHSACR THRQLYALL MAHKREFAGA RFKLRVPAWG RCLRTHSSSA NPNADIILEA ALSELPTEAW PMMQGAVNFS TL

UniProtKB: Replication origin-binding protein

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Macromolecule #2: 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*TP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 22.701482 KDa
SequenceString: (DG)(DG)(DC)(DG)(DC)(DC)(DA)(DG)(DT)(DG) (DC)(DT)(DC)(DG)(DC)(DA)(DC)(DT)(DT)(DC) (DG)(DC)(DC)(DC)(DT)(DA)(DA)(DT)(DA) (DA)(DT)(DA)(DT)(DA)(DT)(DT)(DG)(DG)(DG) (DA) (DC)(DG)(DA)(DA)(DG)(DT) ...String:
(DG)(DG)(DC)(DG)(DC)(DC)(DA)(DG)(DT)(DG) (DC)(DT)(DC)(DG)(DC)(DA)(DC)(DT)(DT)(DC) (DG)(DC)(DC)(DC)(DT)(DA)(DA)(DT)(DA) (DA)(DT)(DA)(DT)(DA)(DT)(DT)(DG)(DG)(DG) (DA) (DC)(DG)(DA)(DA)(DG)(DT)(DG)(DC) (DG)(DA)(DA)(DC)(DG)(DC)(DT)(DT)(DC)(DG) (DC)(DG) (DT)(DT)(DC)(DT)(DC)(DA)(DC) (DT)(DT)(DC)(DT)(DT)(DT)(DT)

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

MacromoleculeName: DNA (5'-D(P*AP*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: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 22.933703 KDa
SequenceString: (DA)(DA)(DA)(DA)(DG)(DA)(DA)(DG)(DT)(DG) (DA)(DG)(DA)(DA)(DC)(DG)(DC)(DG)(DA)(DA) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DC)(DA) (DC)(DT)(DT)(DC)(DG)(DT)(DC)(DC)(DC)(DA) (DA) (DT)(DA)(DT)(DA)(DT)(DT) ...String:
(DA)(DA)(DA)(DA)(DG)(DA)(DA)(DG)(DT)(DG) (DA)(DG)(DA)(DA)(DC)(DG)(DC)(DG)(DA)(DA) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DC)(DA) (DC)(DT)(DT)(DC)(DG)(DT)(DC)(DC)(DC)(DA) (DA) (DT)(DA)(DT)(DA)(DT)(DT)(DA)(DT) (DT)(DA)(DG)(DG)(DG)(DC)(DG)(DA)(DA)(DG) (DT)(DG) (DC)(DG)(DA)(DG)(DC)(DA)(DC) (DT)(DG)(DG)(DC)(DG)(DC)(DC)

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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: 7.8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride
2.0 mMC4H10O2S2DTT
5.0 vol%C3H8O3Glycerol

Details: 20mM HEPES pH7.8, 150mM NaCl, 5mM MgCl2, 2mM DTT, 5vol% Glycerol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 293067
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9hgi:
HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region

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