CryoEM structure of Ku homodimer in complex with linear DNA

2026-04-08 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 INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2023-12-21 2025-12-10 2025-12-10 2026-04-08 National Health and Medical Research Council (NHMRC, Australia) APP2000934 Australia Science and Engineering Research Board (SERB) CRG/2020/002622 India CryoEM structure of Ku homodimer in complex with linear DNA Baral J Rouiller I Das AK NHEJ, DNA repair, Mycobacterium tuberculosis, DNA synapsis, DNA BINDING PROTEIN Baral J Ang CS McMillan PJ Shobhana K Saini A Hinde E Das AK Rouiller I Bringing the ends together: cryo-EM structures of mycobacterial Ku in complex with DNA define its role in NHEJ synapsis. Nucleic Acids Res. UK 54 2026 41521670 doi:10.1093/nar/gkaf1418 1362-4962 0389 NARHAD EMD-43184 other EM volume 8vf5 FULLOVERLAP EMDB EMD-43184 other EM volume EMDB EMD-43186 associated EM volume

Ku homodimer from M.tubeculosis in complex with linear DNA Ku homodimer from M.tubeculosis in complex with linear DNA 0 1 2 3

Protein: Ku homodimer was recombination purified DNA: Chemically Synthesized

Mycobacterium tuberculosis H37Rv Non-homologous end joining protein Ku Mycobacterium tuberculosis H37Rv 0.033609898 2 Escherichia coli BL21(DE3) LEVO MGHHHHHHHHHHSSGHIEGRHMMRAIWTGSIAFGLVNVPVKVYSATADHDIRFHQVHAKDNGRIRYKRVCEACGEVVDYR DLARAYESGDGQMVAITDDDIASLPEERSREIEVLEFVPAADVDPMMFDRSYFLEPDSKSSKSYVLLAKTLAETDRMAIV HFTLRNKTRLAALRVKDFGKREVMMVHTLLWPDEIRDPDFPVLDQKVEIKPAELKMAGQVVDSMADDFNPDRYHDTYQEQ LQELIDTKLEGGQAFTAEDQPRLLDEPEDVSDLLAKLEASVKARSKANSNVPTPP P9WKD9 DNA (40-MER) synthetic construct 0.012239797 1 (DC)(DC)(DC)(DC)(DC)(DC)(DT)(DG)(DT)(DC)(DG)(DC)(DC)(DG)(DC)(DC)(DG)(DA)(DC)(DG) (DT)(DC)(DT)(DG)(DT)(DG)(DA)(DT)(DA)(DT)(DG)(DG)(DC)(DG)(DT)(DT)(DG)(DT)(DT)(DG) DNA DNA (40-MER) synthetic construct 0.012391955999999999 1 (DC)(DA)(DA)(DC)(DA)(DA)(DC)(DG)(DC)(DC)(DA)(DT)(DA)(DT)(DC)(DA)(DC)(DA)(DG)(DA) (DC)(DG)(DT)(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DG)(DA)(DC)(DA)(DG)(DG)(DG)(DG)(DG)(DG) DNA singleParticle particle 0.35 7.5 50.0 HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) 150.0 Sodium chloride 2.0 Tris(2-carboxyethyl)phosphine hydrochloride

50mM HEPES, 150mM NaCl, 2mM TCEP

C-flat-1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 60 AIR ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 4681 40.0 1 5967886 cryoSPARC

Peformed in CryoSPARC Patch CTF

PHASE FLIPPING AND AMPLITUDE CORRECTION Alphafold ID: AF-P9WKD9-F1 1 C1 FOURIER SPACE 3.7 OTHER cryoSPARC

Mean resolution of the map was 3.25 A, generated using ResMap Respective histogram and 2D slices can be provided on request.

635411 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 3 cryoSPARC emd_43186.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 88 95 103 164 172 159 88 95 103 73.304 79.135 85.799 90.0 90.0 90.0 X Y Z -15.707390999999999 20.762978 0.09359611 1.3448192 0.833 0.833 0.83300006 1.0 AUTHOR ::::EMDATABANK.org::::EMD-43186:::: Map obtained after using a 10 A mask on the density modified map. Mentioned maps are also provided. AF-P9WKD9-F1 AlphaFold in silico model RIGID BODY FIT REAL emd_43186_msk_1.map emd_43186_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 109 100 190 159 167 116 190 100 109 158.27 83.3 90.797 90.0 90.0 90.0 Z Y X -15.707390999999999 21.687346999999999 0.000000000015188 1.0 0.833 0.833 0.83299994 AUTHOR ::::EMDATABANK.org::::EMD-43186:::: Unique part of the raw map obtained by boxing and density modification emd_43186_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 349.86002 349.86002 349.86002 90.0 90.0 90.0 X Y Z -0.7818107 1.1476084 0.000012085415 0.012966826 0.83300006 0.83300006 0.83300006 AUTHOR ::::EMDATABANK.org::::EMD-43186:::: Raw full map - used for boxing and density modification. emd_43186_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 349.86002 349.86002 349.86002 90.0 90.0 90.0 X Y Z -0.14662498 0.36132878 0.00007734736 0.011232436 0.83300006 0.83300006 0.83300006 AUTHOR ::::EMDATABANK.org::::EMD-43186:::: Raw half map B emd_43186_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 349.86002 349.86002 349.86002 90.0 90.0 90.0 X Y Z -0.15933542 0.35241005 0.00007707987 0.011252172 0.83300006 0.83300006 0.83300006 AUTHOR ::::EMDATABANK.org::::EMD-43186:::: Raw half map A