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- EMDB-52149: Focused map of dimer 2 of HSV-1 Origin Binding Protein tetramer i... -

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Basic information

Entry
Database: EMDB / ID: EMD-52149
TitleFocused map of dimer 2 of HSV-1 Origin Binding Protein tetramer in complex with single-stranded DNA recognition sites Box 1 and Box 3 with 10 dT-tail
Map data
Sample
  • Complex: HSV-1 Origin Binding Protein tetramer in complex with single-stranded DNA recognition sites Box 1 and Box 3 with 10 dT-tail
    • Protein or peptide: Origin Binding Protein
KeywordsDNA / Helicase / Complex / DNA BINDING PROTEIN
Biological speciesHuman alphaherpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 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.
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_52149.png

Downloads & links

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Map

FileDownload / File: emd_52149.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: 0.2
Minimum - Maximum-0.37427855 - 0.83179724
Average (Standard dev.)0.0015550159 (±0.023966474)
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_52149_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_52149_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52149_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52149_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HSV-1 Origin Binding Protein tetramer in complex with single-stra...

EntireName: HSV-1 Origin Binding Protein tetramer in complex with single-stranded DNA recognition sites Box 1 and Box 3 with 10 dT-tail
Components
  • Complex: HSV-1 Origin Binding Protein tetramer in complex with single-stranded DNA recognition sites Box 1 and Box 3 with 10 dT-tail
    • Protein or peptide: Origin Binding Protein

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Supramolecule #1: HSV-1 Origin Binding Protein tetramer in complex with single-stra...

SupramoleculeName: HSV-1 Origin Binding Protein tetramer in complex with single-stranded DNA recognition sites Box 1 and Box 3 with 10 dT-tail
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS

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Macromolecule #1: Origin Binding Protein

MacromoleculeName: Origin Binding Protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPFVGGAESG DPLGAGRPIG DDECEQYTSS VSLARMLYGG DLAEWVPRVH PKTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTTA LIRWLREAIH SPDTSVLVVS CRRSFTQTLA TRFAESGLVD FVTYFSSTNY IMNDRPFHRL IVQVESLHRV GPNLLNNYDV ...String:
MPFVGGAESG DPLGAGRPIG DDECEQYTSS VSLARMLYGG DLAEWVPRVH PKTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTTA LIRWLREAIH SPDTSVLVVS CRRSFTQTLA TRFAESGLVD FVTYFSSTNY IMNDRPFHRL IVQVESLHRV GPNLLNNYDV LVLDEVMSTL GQLYSPTMQQ LGRVDALMLR LLRTCPRIIA MDATANAQLV DFLCGLRGEK NVHVVVGEYA MPGFSARRCL FLPRLGTELL QAALRPPGPP SGPSPDASPD ARGATFFGEL EARLGGGDNI CIFSSTVSFA EIVARFCRQF TDRVLLLHSL TPLGDVTTWG QYRVVIYTTV VTVGLSFDPL HFDGMFAYVK PMNYGPDMVS VYQSLGRVRT LRKGELLIYM DGSGARSEPV FTPMLLNHVV SSCGQWPAQF SQVTNLLCRR FKGRCDASAC DTSLGRGSRI YNKFRYKHYF ERCTLACLSD SLNILHMLLT LNCIRVRFWG HDDTLTPKDF CLFLRGVHFD ALRAQRDLRE LRCRDPEASL PAQAAETEEV GLFVEKYLRS DVAPAEIVAL MRNLNSLMGR TRFIYLALLE ACLRVPMATR SSAIFRRIYD HYATGVIPTI NVTGELELVA LPPTLNVTPV WELLCLCSTM AARLHWDSAA GGSGRTFGPD DVLDLLTPHY DRYMQLVFEL GHCNVTDGLL LSEEAVKRVA DALSGCPPRG SVSETDHAVA LFKIIWGELF GVQMAKSTQT FPGAGRVKNL TKQTIVGLLD AHHIDHSACR THRQLYALLM AHKREFAGAR FKLRVPAWGR CLRTHSSSAN PNADIILEAA LSELPTEAWP MMQGAVNFST L

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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: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 95006
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

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