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- EMDB-45042: Two-subunit asymmetric unit of Epstein-Barr virus annealase BALF2... -

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Basic information

Entry
Database: EMDB / ID: EMD-45042
TitleTwo-subunit asymmetric unit of Epstein-Barr virus annealase BALF2 ssDNA-annealing complex
Map data
Sample
  • Complex: Asymmetric subunit of the BALF2 ssDNA-annealing filament
    • Protein or peptide: Major DNA-binding protein
    • DNA: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
    • DNA: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
  • Ligand: ZINC ION
  • Ligand: water
KeywordsRecombinase / annealase / SSB / Filament / Homologous Recombination / 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
Major DNA-binding protein
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsNicholls J / Tolun G / Brewster J
Funding support Australia, 1 items
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, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45042.png

Downloads & links

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Map

FileDownload / File: emd_45042.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048
Minimum - Maximum-0.18881114 - 0.6148421
Average (Standard dev.)0.0015061735 (±0.017563965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45042_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45042_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45042_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Asymmetric subunit of the BALF2 ssDNA-annealing filament

EntireName: Asymmetric subunit of the BALF2 ssDNA-annealing filament
Components
  • Complex: Asymmetric subunit of the BALF2 ssDNA-annealing filament
    • Protein or peptide: Major DNA-binding protein
    • DNA: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')
    • DNA: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Asymmetric subunit of the BALF2 ssDNA-annealing filament

SupramoleculeName: Asymmetric subunit of the BALF2 ssDNA-annealing filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8

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Macromolecule #1: Major DNA-binding protein

MacromoleculeName: Major DNA-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: B95-8
Molecular weightTheoretical: 123.247445 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQGAQTSEDN LGSQSQPGPC GYIYFYPLAT YPLREVATLG TGYAGHRCLT VPLLCGITVE PGFSINVKAL HRRPDPNCGL LRATSYHRD IYVFHNAHMV PPIFEGPGLE ALCGETREVF GYDAYSALPR ESSKPGDFFP EGLDPSAYLG AVAITEAFKE R LYSGNLVA ...String:
MQGAQTSEDN LGSQSQPGPC GYIYFYPLAT YPLREVATLG TGYAGHRCLT VPLLCGITVE PGFSINVKAL HRRPDPNCGL LRATSYHRD IYVFHNAHMV PPIFEGPGLE ALCGETREVF GYDAYSALPR ESSKPGDFFP EGLDPSAYLG AVAITEAFKE R LYSGNLVA IPSLKQEVAV GQSASVRVPL YDKEVFPEGV PQLRQFYNSD LSRCMHEALY TGLAQALRVR RVGKLVELLE KQ SLQDQAK VAKVAPLKEF PASTISHPDS GALMIVDSAA CELAVSYAPA MLEASHETPA SLNYDSWPLF ADCEGPEARV AAL HRYNAS LAPHVSTQIF ATNSVLYVSG VSKSTGQGKE SLFNSFYMTH GLGTLQEGTW DPCRRPCFSG WGGPDVTGTN GPGN YAVEH LVYAASFSPN LLARYAYYLQ FCQGQKSSLT PVPETGSYVA GAAASPMCSL CEGRAPAVCL NTLFFRLRDR FPPVM STQR RDPYVISGAS GSYNETDFLG NFLNFIDKED DGQRPDDEPR YTYWQLNQNL LERLSRLGID AEGKLEKEPH GPRDFV KMF KDVDAAVDAE VVQFMNSMAK NNITYKDLVK SCYHVMQYSC NPFAQPACPI FTQLFYRSLL TILQDISLPI CMCYEND NP GLGQSPPEWL KGHYQTLCTN FRSLAIDKGV LTAKEAKVVH GEPTCDLPDL DAALQGRVYG RRLPVRMSKV LMLCPRNI K IKNRVVFTGE NAALQNSFIK STTRRENYII NGPYMKFLNT YHKTLFPDTK LSSLYLWHNF SRRRSVPVPS GASAEEYSD LALFVDGGSR AHEESNVIDV VPGNLVTYAK QRLNNAILKA CGQTQFYISL IQGLVPRTQS VPARDYPHVL GTRAVESAAA YAEATSSLT ATTVVCAATD CLSQVCKARP VVTLPVTINK YTGVNGNNQI FQAGNLGYFM GRGVDRNLLQ APGAGLRKQA G GSSMRKKF VFATPTLGLT VKRRTQAATT YEIENIRAGL EAIISQKQEE DCVFDVVCNL VDAMGEACAS LTRDDAEYLL GR FSVLADS VLETLATIAS SGIEWTAEAA RDFLEGVWGG PGAAQDNFIS VAEPVSTASQ ASAGLLLGGG GQGSGGRRKR RLA TVLPGL EV

UniProtKB: Major DNA-binding protein

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Macromolecule #2: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3')

MacromoleculeName: DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3') / type: dna / ID: 2 / Details: single-stranded DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.632382 KDa
SequenceString:
(DG)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DG)(DC) (DC)(DC)

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Macromolecule #3: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3') / type: dna / ID: 3 / Details: single-stranded DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.643388 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DC)(DG)(DA)(DT)(DT)(DT) (DT)(DT)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 475 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 9
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
6.0 mMC2H6OSbeta-mercaptoethanol
10.0 mMMgCl2Magnesium Chloride
20.0 mMC4H12ClNO3Tris Hydrochloride

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
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00039000000000000005 kPa / Details: 0.15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample formed flexible helical assemblies

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
DetailsPreliminary Grid screening was performed manually
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 6248 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3311483
CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Software - details: Local Refinement
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.
Number images used: 557352
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) / Software - details: Homogenous Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) / Software - details: Local Refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 463880 / Software - Name: cryoSPARC (ver. 4) / Software - details: HeteroRefinement / Details: Hetero Refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial 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.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9byq:
Two-subunit asymmetric unit of Epstein-Barr virus annealase BALF2 ssDNA-annealing complex

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