2025-06-11 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2024-05-24 2025-06-11 2025-06-11 2025-06-11 National Health and Medical Research Council (NHMRC, Australia) GNT1184012 Australia Two-subunit asymmetric unit of Epstein-Barr virus annealase BALF2 ssDNA-annealing complex Nicholls J Tolun G Brewster J Recombinase, annealase, SSB, Filament, Homologous Recombination, RECOMBINATION Nicholls J Brewster J Tolun G Structural determination of BALF2 annealing intermediate reveals the mechanism through which DNA annealing occurs To Be Published 0353 9byq FULLOVERLAP Asymmetric subunit of the BALF2 ssDNA-annealing filament Asymmetric subunit of the BALF2 ssDNA-annealing filament 0 1 2 3 human gammaherpesvirus 4 B95-8 Major DNA-binding protein human gammaherpesvirus 4 B95-8 0.123247445 4 Spodoptera frugiperda LEVO MQGAQTSEDNLGSQSQPGPCGYIYFYPLATYPLREVATLGTGYAGHRCLTVPLLCGITVEPGFSINVKALHRRPDPNCGL LRATSYHRDIYVFHNAHMVPPIFEGPGLEALCGETREVFGYDAYSALPRESSKPGDFFPEGLDPSAYLGAVAITEAFKER LYSGNLVAIPSLKQEVAVGQSASVRVPLYDKEVFPEGVPQLRQFYNSDLSRCMHEALYTGLAQALRVRRVGKLVELLEKQ SLQDQAKVAKVAPLKEFPASTISHPDSGALMIVDSAACELAVSYAPAMLEASHETPASLNYDSWPLFADCEGPEARVAAL HRYNASLAPHVSTQIFATNSVLYVSGVSKSTGQGKESLFNSFYMTHGLGTLQEGTWDPCRRPCFSGWGGPDVTGTNGPGN YAVEHLVYAASFSPNLLARYAYYLQFCQGQKSSLTPVPETGSYVAGAAASPMCSLCEGRAPAVCLNTLFFRLRDRFPPVM STQRRDPYVISGASGSYNETDFLGNFLNFIDKEDDGQRPDDEPRYTYWQLNQNLLERLSRLGIDAEGKLEKEPHGPRDFV KMFKDVDAAVDAEVVQFMNSMAKNNITYKDLVKSCYHVMQYSCNPFAQPACPIFTQLFYRSLLTILQDISLPICMCYEND NPGLGQSPPEWLKGHYQTLCTNFRSLAIDKGVLTAKEAKVVHGEPTCDLPDLDAALQGRVYGRRLPVRMSKVLMLCPRNI KIKNRVVFTGENAALQNSFIKSTTRRENYIINGPYMKFLNTYHKTLFPDTKLSSLYLWHNFSRRRSVPVPSGASAEEYSD LALFVDGGSRAHEESNVIDVVPGNLVTYAKQRLNNAILKACGQTQFYISLIQGLVPRTQSVPARDYPHVLGTRAVESAAA YAEATSSLTATTVVCAATDCLSQVCKARPVVTLPVTINKYTGVNGNNQIFQAGNLGYFMGRGVDRNLLQAPGAGLRKQAG GSSMRKKFVFATPTLGLTVKRRTQAATTYEIENIRAGLEAIISQKQEEDCVFDVVCNLVDAMGEACASLTRDDAEYLLGR FSVLADSVLETLATIASSGIEWTAEAARDFLEGVWGGPGAAQDNFISVAEPVSTASQASAGLLLGGGGQGSGGRRKRRLA TVLPGLEV P03227 DNA(5'-D(*GP*CP*AP*GP*AP*AP*TP*CP*GP*CP*CP*C)-3') synthetic construct 0.003632382
single-stranded DNA
1 (DG)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DG)(DC)(DC)(DC) DNA DNA(5'-D(*AP*GP*CP*TP*CP*GP*AP*TP*TP*TP*TP*T)-3') synthetic construct 0.0036433879999999996
single-stranded DNA
1 (DA)(DG)(DC)(DT)(DC)(DG)(DA)(DT)(DT)(DT)(DT)(DT) DNA ZINC ION 6.5409e-05 2 ZN water 1.8015e-05 475 HOH singleParticle filament 0.9 9.0 100.0 NaCl Sodium Chloride 6.0 C2H6OS beta-mercaptoethanol 10.0 MgCl2 Magnesium Chloride 20.0 C4H12ClNO3 Tris Hydrochloride
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
 UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE AIR 0.00039000000000000005
0.15 mA
 ETHANE 100 295 FEI VITROBOT MARK IV
The sample formed flexible helical assemblies
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 1.5 NITROGEN GIF Bioquantum 15
Preliminary Grid screening was performed manually
GATAN K3 (6k x 4k) 5760 4092 2 6248 65.0 1 3311483 cryoSPARC 4 Patch CTF PHASE FLIPPING AND AMPLITUDE CORRECTION Alphafold2 C2 BACK PROJECTION 2.2 FSC 0.143 CUT-OFF cryoSPARC 4 Local Refinement
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.
557352 MAXIMUM LIKELIHOOD cryoSPARC 4 Homogenous Refinement MAXIMUM LIKELIHOOD cryoSPARC 4 Local Refinement 2 463880.0 cryoSPARC 4 HeteroRefinement
Hetero Refinement
 emd_45042.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.18881114 0.6148421 0.0015061735 0.017563965 0.84 0.84 0.84 0.048 AUTHOR AlphaFold in silico model FLEXIBLE FIT
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.
REAL emd_45042_msk_1.map emd_45042_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.3154986 0.6823387 0.0006228518 0.038837787 0.84 0.84 0.84 AUTHOR emd_45042_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.26183063 0.759998 0.0006175447 0.0389084 0.84 0.84 0.84 AUTHOR