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- PDB-9byq: Two-subunit asymmetric unit of Epstein-Barr virus annealase BALF2... -

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Basic information

Entry
Database: PDB / ID: 9byq
TitleTwo-subunit asymmetric unit of Epstein-Barr virus annealase BALF2 ssDNA-annealing complex
Components
  • DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
  • DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
  • Major DNA-binding protein
KeywordsRECOMBINATION / Recombinase / annealase / SSB / Filament / Homologous Recombination
Function / homology
Function and homology information


viral tegument / bidirectional double-stranded viral DNA replication / single-stranded DNA binding / DNA replication / host cell nucleus
Similarity search - Function
Viral ssDNA-binding protein / DBP-like superfamily / Viral ssDNA binding protein, head domain / ssDNA binding protein
Similarity search - Domain/homology
DNA / DNA (> 10) / Major DNA-binding protein
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsNicholls, J. / Tolun, G. / Brewster, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1184012 Australia
CitationJournal: To Be Published
Title: Structural determination of BALF2 annealing intermediate reveals the mechanism through which DNA annealing occurs
Authors: Nicholls, J. / Brewster, J. / Tolun, G.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major DNA-binding protein
C: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
B: Major DNA-binding protein
F: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
D: Major DNA-binding protein
E: Major DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,3968
Polymers500,2666
Non-polymers1312
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Cryo-EM + Negative-Staining EM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Major DNA-binding protein


Mass: 123247.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: DBP, BALF2 / Plasmid: bMON14272 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovarian / References: UniProt: P03227
#2: DNA chain DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')


Mass: 3632.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')


Mass: 3643.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Asymmetric subunit of the BALF2 ssDNA-annealing filament
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9 / Cell: Ovarian / Plasmid: bMON14272
Buffer solutionpH: 9
Details: Sample incubated for 30 minutes at 37 degrees Celsius and then for 20 hours at 4 degrees Celsius, in the presence of 1.83 uM oligonucleotide
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium ChlorideNaCl1
26 mMbeta-mercaptoethanolC2H6OS1
310 mMMagnesium ChlorideMgCl21
420 mMTris HydrochlorideC4H12ClNO31
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample formed flexible helical assemblies
Specimen supportDetails: 0.15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Preliminary Grid screening was performed manually
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6248
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4particle selectionBlob Picker followed by Template Picker
2EPU3image acquisitionUsed to automate collection
3cryoSPARC4image acquisitionUsed to process images
5cryoSPARC4CTF correctionPatch CTF
8ISOLDE1.3model fitting
10PHENIX1.2.1model refinementWinPHENIX
12cryoSPARC4initial Euler assignmentHomogenous Refinement
13cryoSPARC4final Euler assignmentLocal Refinement
14cryoSPARC4classificationHeteroRefinement
15cryoSPARC43D reconstructionLocal Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3311483
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 557352 / Algorithm: BACK PROJECTION
Details: Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA sequences. The actual DNA sequences bound to each subunit are ...Details: Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA sequences. The actual DNA sequences bound to each subunit are different between particles and are lost during particle averaging. Different sequences were built in to the density based on areas of highest complementarity of the substrate.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial fitting was done in isolde before refinement in Phenix. Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA ...Details: Initial fitting was done in isolde before refinement in Phenix. Though C2 symmetry was applied to the map, the actual structure is not C2. This is primarily because of differences in the DNA sequences. The actual DNA sequences bound to each subunit are different between particles and are lost during particle averaging. Different sequences were built in to the density based on areas of highest complementarity of the substrate.
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038796
ELECTRON MICROSCOPYf_angle_d0.52111957
ELECTRON MICROSCOPYf_dihedral_angle_d4.611230
ELECTRON MICROSCOPYf_chiral_restr0.0411321
ELECTRON MICROSCOPYf_plane_restr0.0051576

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