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- PDB-9hgj: HSV-1 Origin Binding Protein in complex with double-stranded DNA ... -

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Basic information

Entry
Database: PDB / ID: 9hgj
TitleHSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS and non-hydrolyzable ATP analog
Components
  • 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')
  • 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')
  • Replication origin-binding protein
KeywordsDNA BINDING PROTEIN / DNA / Helicase / Complex
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / DNA / DNA (> 10) / Replication origin-binding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain KOS
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsGustavsson, E. / Grunewald, K. / Elias, P. / Hallberg, B.M.
Funding support Sweden, Germany, 2items
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, B.M.
History
DepositionNov 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication origin-binding protein
B: Replication origin-binding protein
C: 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')
D: 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1857
Polymers239,1144
Non-polymers1,0713
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Replication origin-binding protein / OriBP


Mass: 94887.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain KOS / Gene: UL9, HHV1gp016, hmpv214_0009 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3YPE9
#2: DNA chain 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')


Mass: 24553.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: GenBank: 2582897638
#3: DNA chain 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')


Mass: 24785.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: GenBank: 2582897638
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS and non-hydrolyzable ATP analog
Type: COMPLEX / Entity ID: #2-#3 / Source: RECOMBINANT
Source (natural)Organism: Human alphaherpesvirus 1 strain KOS
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.8
Details: 20mM HEPES pH7.8, 150mM NaCl, 5mM MgCl2, 2mM DTT, 5vol% Glycerol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
42 mMDTTC4H10O2S21
55 vol%GlycerolC3H8O31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.92model fitting
9cryoSPARC3.2initial Euler assignment
10cryoSPARC3.2final Euler assignment
12cryoSPARC3.23D reconstruction
19Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226401 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9HGI

9hgi


Accession code: 9HGI / Source name: PDB / Type: experimental model
RefinementResolution: 3.53→3.53 Å / Cor.coef. Fo:Fc: 0.909 / SU B: 22.691 / SU ML: 0.343 / ESU R: 0.697
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.32671 --
obs0.32671 91462 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 191.798 Å2
Refinement stepCycle: 1 / Total: 13666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01214120
ELECTRON MICROSCOPYr_bond_other_d00.01612843
ELECTRON MICROSCOPYr_angle_refined_deg1.8961.82919348
ELECTRON MICROSCOPYr_angle_other_deg0.6651.73329494
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.7115.1111855
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.3225131
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.691102102
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1310.2042233
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0216055
ELECTRON MICROSCOPYr_gen_planes_other0.0010.023287
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it20.86317.8666457
ELECTRON MICROSCOPYr_mcbond_other20.86317.8666457
ELECTRON MICROSCOPYr_mcangle_it33.41732.2748059
ELECTRON MICROSCOPYr_mcangle_other33.41632.2778060
ELECTRON MICROSCOPYr_scbond_it22.60621.0537663
ELECTRON MICROSCOPYr_scbond_other22.60621.0537663
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other37.18437.89511290
ELECTRON MICROSCOPYr_long_range_B_refined55.307235.4354056
ELECTRON MICROSCOPYr_long_range_B_other55.306235.4454057
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.364 6816 -
obs--100 %

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