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- PDB-9byr: Filamentous Epstein-Barr virus annealase BALF2 ssDNA-annealing complex -

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Basic information

Entry
Database: PDB / ID: 9byr
TitleFilamentous 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/DNA / Recombinase / annealase / SSB / Filament / Homologous Recombination / RECOMBINATION / RECOMBINATION-DNA complex
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: 7.75 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
N: Major DNA-binding protein
M: Major DNA-binding protein
n: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
L: Major DNA-binding protein
l: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
O: Major DNA-binding protein
o: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
K: Major DNA-binding protein
k: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
P: Major DNA-binding protein
p: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
J: Major DNA-binding protein
j: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
Q: Major DNA-binding protein
q: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
I: Major DNA-binding protein
i: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
R: Major DNA-binding protein
r: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
H: Major DNA-binding protein
h: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
S: Major DNA-binding protein
s: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
G: Major DNA-binding protein
g: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
T: Major DNA-binding protein
t: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
F: Major DNA-binding protein
f: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
U: Major DNA-binding protein
u: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
E: Major DNA-binding protein
e: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
V: Major DNA-binding protein
v: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
D: Major DNA-binding protein
d: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
W: Major DNA-binding protein
w: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
C: Major DNA-binding protein
c: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
X: Major DNA-binding protein
x: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
B: Major DNA-binding protein
A: Major DNA-binding protein
b: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,039,41168
Polymers3,037,97246
Non-polymers1,43922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Assembly observed by Negative-Staining EM and Cryo-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.: 24
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.: 11 / Source method: obtained synthetically / 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.: 11 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Zn
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: Epstein-Barr virus recombinase BALF2 filamentous ssDNA-annealing complex
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: Quantifoil R1.2/1.3 + 2nm continuous carbon were also used for collection
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: 11747
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 selectionTemplate Picker
2EPU3image acquisitionUsed to automate collection
3cryoSPARC4image acquisitionUsed to process images
5cryoSPARC4CTF correctionPatch CTF
8UCSF ChimeraX1.7model fitting
10cryoSPARC4initial Euler assignmentHelical Refinement without symmetry
11cryoSPARC4final Euler assignmentHelical Refinement without symmetry
12cryoSPARC4classification2D classification
13cryoSPARC43D reconstructionLocal Refinement
14PHENIX2model refinementModel passed through Phenix with all refinement options turned off in preparation for pdb deposition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 961513
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278657 / Num. of class averages: 36 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: Protein was rigid-fit using chimeraX
Atomic model buildingDetails: Assymetric Unit was determined to a high-resolution via local refinement and then rigid-fit into low-resolution map
Source name: Other / Type: experimental model
RefinementCross valid method: NONE

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