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

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Basic information

Entry
Database: PDB / ID: 9hgi
TitleHSV-1 Origin Binding Protein in complex with double-stranded DNA recognition sequence OriS with 6 basepairs removed from the AT-rich region
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
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: 2.77 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.
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')


Theoretical massNumber of molelcules
Total (without water)236,9894
Polymers236,9894
Non-polymers00
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: 95677.102 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: 22701.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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: 22933.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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 with 6 basepairs removed from the AT-rich region
Type: COMPLEX / Entity ID: all / 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: 50 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
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293067 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementResolution: 2.77→2.77 Å / Cor.coef. Fo:Fc: 0.876 / SU B: 8.645 / SU ML: 0.16 / ESU R: 0.294
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31901 --
obs0.31901 177112 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 149.973 Å2
Refinement stepCycle: 1 / Total: 13657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01214116
ELECTRON MICROSCOPYr_bond_other_d00.01612872
ELECTRON MICROSCOPYr_angle_refined_deg1.7551.82819324
ELECTRON MICROSCOPYr_angle_other_deg0.5941.73329558
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.6835.1481867
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.2395132
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.903102113
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1140.2052230
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0216109
ELECTRON MICROSCOPYr_gen_planes_other0.0010.023299
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_it14.36613.2126488
ELECTRON MICROSCOPYr_mcbond_other14.36613.2126488
ELECTRON MICROSCOPYr_mcangle_it22.64123.8888103
ELECTRON MICROSCOPYr_mcangle_other22.63923.898104
ELECTRON MICROSCOPYr_scbond_it16.2917.6257628
ELECTRON MICROSCOPYr_scbond_other16.28917.6257628
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other26.14931.63711222
ELECTRON MICROSCOPYr_long_range_B_refined42.535197.4158702
ELECTRON MICROSCOPYr_long_range_B_other42.534197.4358703
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.476 13063 -
obs--100 %

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