Cryo-EM structure of Z22 mAb in complex with left-handed Z-DNA (dimer of trimer)

2026-01-14 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-12-02 2026-01-14 2026-01-14 2026-01-14 Ministry of Education (MoE, Singapore) Singapore Cryo-EM structure of Z22 mAb in complex with left-handed Z-DNA (dimer of trimer) Chin DHR Luo YB Luo D Z-DNA, monoclonal antibody, antibody avidity, left-handed geometry, DNA BINDING PROTEIN Chin D Luo Y Lau Y Dutta N He Z Yin C Williams RM Balachandran S Vicens Q Droge P Luo D Cryo-EM structures of anti Z-DNA antibodies in complex with antigen reveal distinct recognition modes of a left-handed geometry. Biorxiv US 2025 41415447 doi:10.64898/2025.12.12.693871 2692-8205 9tgo FULLOVERLAP EMDB EMD-55906 associated EM volume

Dimer of trimer complex of Z22 antibody with left-handed Z-DNA Dimer of trimer complex of Z22 antibody with left-handed Z-DNA 0 1 2 3

Full length antibody arranged as a dimer of trimer around the Z-DNA

Mus musculus 0.9 Z22-VH Mus musculus 0.013627357

Heavy chain of Z22

6 Homo sapiens LEVO KVQLVESGGGLVQPKGSLKLSCAASGFNFNTYAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSMKDRFTISRDDSENM LYLQMINLKAEDTAMYYCVRQAYSNYGAMDYWGQGISVTVS Z22-VL Mus musculus 0.011662902

Light chain of Z22

6 Homo sapiens LEVO DIQMTQTISSLSASLGDRVTISCSASQGISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEP EDIATYFCQQYSKFPFTFGSGTKLEI DNA (5'-D(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3') Homo sapiens 0.0036653679999999996

DNA chemically synthesised from IDT

4 (DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG) DNA MAGNESIUM ION 2.4305e-05 15 MG water 1.8015e-05 32 HOH singleParticle particle 1.1 7.2 20.0 HEPES 150.0 NaCl 1.0 sucrose

High salt buffer for complex preparation: 20mM HEPES pH 7.2, 2.5M NaCl, 0.7mM MgCl2 Buffer above is for analytical SEC.

Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE 60 ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.23 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 4660 50.0 1 cryoSPARC 4.5 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.8 FSC 0.143 CUT-OFF cryoSPARC 4.5 59879 NOT APPLICABLE NOT APPLICABLE emd_55906.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 273.6 273.6 273.6 90.0 90.0 90.0 X Y Z -0.18784851 0.3915121 0.00016784902 0.007933968 0.76 0.76 0.76 0.02 AUTHOR ::::EMDATABANK.org::::EMD-55906:::: emd_55906_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 273.6 273.6 273.6 90.0 90.0 90.0 X Y Z -0.33370098 0.32297638 0.00018558794 0.039868373 0.76 0.76 0.76 AUTHOR ::::EMDATABANK.org::::EMD-55906:::: emd_55906_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 273.6 273.6 273.6 90.0 90.0 90.0 X Y Z -0.31610775 0.40840662 0.00018485569 0.039875854 0.76 0.76 0.76 AUTHOR ::::EMDATABANK.org::::EMD-55906::::