Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with J9 fab

2026-04-01 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2025-03-14 2026-04-01 2026-04-01 2026-04-01 Science and Engineering Research Board (SERB) SPG/2021/002433 India Department of Biotechnology (DBT, India) IA/I/22/1/506233 India Helical Reconstruction of DENV2 THSTI/TRC/01 tubular particles bound with J9 fab Roy A Prasad VM Dengue virus, neutralizing antibody binding, fab-virus complex, E-protein, helical, flavivirus, VIRUS, VIRAL PROTEIN-IMMUNE SYSTEM complex Chatterjee A Roy A Srinivasan S Charles S Lubow J Goo L Prasad VM Structural determinants of broadly neutralizing human antibodies binding to morphological dengue virus variants. To Be Published 0353 EMD-63759 other EM volume EMD-63762 other EM volume EMD-63763 other EM volume 9mb1 FULLOVERLAP EMDB EMD-63759 other EM volume EMDB EMD-63762 other EM volume EMDB EMD-63763 other EM volume EMDB EMD-63764 associated EM volume

PDB 9MAV unspecified PDB 9MAZ unspecified PDB 9MB0 unspecified dengue virus type 2 bound with J9 fab dengue virus type 2 bound with J9 fab 0 1 2 3

Cultured in C6/36 mosquito cell lines and purified from cell supernatent

dengue virus type 2 1 1 dengue virus type 2 DENV2/THSTI/TRC/01 Homo sapiens VIRION SEROTYPE true false monoclonal antibody J9 1 2 3

Fab fragment generated from papain based proteolytic cleavage of J9 IgG1.

Homo sapiens Envelope Glycoprotein dengue virus type 2 THSTI/TRC/01 0.05426256199999999

sequence refers to UNZ79673.1 genebank

2 LEVO MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTASRCPTQGEP SLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKIVQPENLEYTIVITPHSGEENAVGNDTGKHGK EVKVTPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTI VIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLSWFKKGSSIGQ MFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVVITWIGMNSRSTSLSVSLV LVGVVTLYLGVMVQA J9 Heavy chain variable region Homo sapiens 0.023616317999999997 2 Homo sapiens LEVO QVQLVQSGAEVRKPGSSVKVSCKTSGGSLNSYGISWVRQAPGGQGLEWMGGIIPFFGTVIYSDNYQGRASFSSDESTTTA YMELRSLRSEDTAVYYCARYCYSASCYHNWFDPWGQGTLVTVSTASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEP VTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV J9 Light chain variable region Homo sapiens 0.023693346 2 Homo sapiens LEVO DIVLTQSPATLSLSPGERATLSCRASQSVGSSLAWYQQKPGQAPRLLIYDASKRASGFPARFSGSGSGTDFTLTISSLEP GDFAVYYCQQRSSWPPYMYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSG NSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC helical particle 8.0 10.0 Tris-HCL NTE buffer 120.0 NaCl NTE buffer 1.0 EDTA NTE buffer PELCO Ultrathin Carbon with Lacey Carbon COPPER 400 CARBON LACEY GLOW DISCHARGE 30 ETHANE 90 277 FEI VITROBOT MARK IV

DENV2 virus and J9 fab mixture with Fab in greater amount.

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.25 2.75 36000.0 NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1 3847 48.0 1 2 15.19 80.62 C1 FOURIER SPACE 14.41 FSC 0.143 CUT-OFF cryoSPARC 4.6.0

Residues involved in atom clashes are the part of immunoglobulin constant region which are appearing to be in head on clash with each other on a dimer on which the Fab bind.

5769 RELION 4.0.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 19729 RELION 4.0.1

3D-cylinder geometry

NOT APPLICABLE RELION 4.0.1

Maximum Likelihood

emd_63764.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 649.6 649.6 649.6 90.0 90.0 90.0 X Y Z -0.23624879 1.5402261 0.04142262 0.16495486 4.64 4.64 4.64 0.304 AUTHOR ::::EMDATABANK.org::::EMD-63764:::: Helical Reconstruction of DENV2/THSTI/TRC/01 tubular particles bound with J9V1 map half main map SwissModel in silico model

Edimer

AlphaFold in silico model

J9 fab

RIGID BODY FIT

map-correlation= 0.8595

map correlation emd_63764_msk_1.map emd_63764_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 649.6 649.6 649.6 90.0 90.0 90.0 X Y Z -0.7456623 1.7975576 0.0066018277 0.19137362 4.64 4.64 4.64 AUTHOR ::::EMDATABANK.org::::EMD-63764:::: Helical Reconstruction of DENV2/THSTI/TRC/01 tubular particles bound with J9V1 map half map emd_63764_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 649.6 649.6 649.6 90.0 90.0 90.0 X Y Z -0.6468181 1.8177483 0.005731404 0.1871632 4.64 4.64 4.64 AUTHOR ::::EMDATABANK.org::::EMD-63764:::: Helical Reconstruction of DENV2/THSTI/TRC/01 tubular particles bound with J9V1 map half map