[English] 日本語
Yorodumi
- EMDB-52147: Consensus map of HSV-1 Origin Binding Protein tetramer in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52147
TitleConsensus map 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: 4.34 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

-
Structure visualization

Supplemental images

emd_52147.png

Downloads & links

-
Map

FileDownload / File: emd_52147.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: 0.12
Minimum - Maximum-0.30143175 - 0.7424439
Average (Standard dev.)0.0016091925 (±0.024085758)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_52147_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_52147_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52147_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52147_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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: 4.34 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)

-
Atomic model buiding 1

Initial modelPDB ID:

9hgi


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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more