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- EMDB-52145: HSV-1 Origin Binding Protein in complex with double-stranded DNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52145
TitleHSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS and non-hydrolyzable ATP analog
Map data
Sample
  • Complex: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS and non-hydrolyzable ATP analog
    • 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')
  • Protein or peptide: Replication origin-binding protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
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: 3.53 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: Gustavsson E / Grunewald K / Elias P / Hallberg BM
History
DepositionNov 19, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52145.png

Downloads & links

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Map

FileDownload / File: emd_52145.map.gz / Format: CCP4 / Size: 307.5 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 432 pix.
= 367.2 Å		0.85 Å/pix.
x 432 pix.
= 367.2 Å		0.85 Å/pix.
x 432 pix.
= 367.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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-0.22729097 - 0.50776386
Average (Standard dev.)0.0002955744 (±0.009987751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 367.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52145_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_52145_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52145_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52145_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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 and non-hydrolyzable ATP analog
Components
  • Complex: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS and non-hydrolyzable ATP analog
    • 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')
  • Protein or peptide: Replication origin-binding protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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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 and non-hydrolyzable ATP analog
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
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: 94.887219 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 PMMQ

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: 24.55368 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)(DA)(DT)(DA)(DT) (DA) (DT)(DT)(DG)(DG)(DG)(DA) ...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)(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)

GENBANK: GENBANK: OR428170.1

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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: 24.785898 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)(DA) ...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)(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)

GENBANK: GENBANK: OR428170.1

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 54.0 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: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 226401
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 modelPDB ID:

9hgi


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9hgj:
HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS and non-hydrolyzable ATP analog

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