2026-04-22 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 2025-03-05 2026-04-22 2026-04-22 2026-04-22 Science and Engineering Research Board (SERB) SPG/2021/002433 India Wellcome Trust IA/I/22/1/506233 United Kingdom D14.F25.S02 Fab complexed to DENV2-US/BID/V594/2006 virus (5f-3f map) Chatterjee AC Mangala Prasad V Dengue virus, flavivirus, broadly neutralizing antibody, VIRUS Chatterjee AC Roy A Srinivasan S Charles S Lubow J Goo L Mangala Prasad V Structural determinants of broadly neutralizing human antibodies binding to morphological dengue virus variants. To Be Published 0353 EMD-63809 other EM volume
Helical reconstruction of DENV2 US/BID-V594/2006 bound with D14.F25.SO2 fab
 EMD-63813 other EM volume
2F-3F map of US-BID DENV 2 in complex with D14.F25.S02
 9m5h FULLOVERLAP EMDB EMD-63643 associated EM volume
DENV2-US/BID/V594/2006 in complex with D14.F25.S02 Fab
 EMDB EMD-63809 other EM volume
Helical reconstruction of DENV2 US/BID-V594/2006 bound with D14.F25.SO2 fab
 EMDB EMD-63813 other EM volume
2F-3F map of US-BID DENV 2 in complex with D14.F25.S02
 PDB 9U34 unspecified
Helical reconstruction of DENV2 US/BID-V594/2006 bound with D14.F25.SO2 fab
 PDB 9U38 unspecified
2F-3F map of US-BID DENV 2 in complex with D14.F25.S02
 dengue virus type 2 dengue virus type 2 0 1 2 3 4
CULTURED IN C6/36 MOSQUITO CELL LINES AND PURIFIED FROM CELL SUPERNATANT
dengue virus type 2 US/BID/V594/2006 Homo sapiens VIRION SEROTYPE true false Monoclonal antibody D14.F25.S02 1 2 3
Fab fragment generated from papain based proteolytic cleavage of D14.F25.S02 IgG1
Homo sapiens Envelope Glycoprotein E dengue virus type 2 DENV-2/US/BID-V594/2006 0.054413789
Envelope protein E
3 LEVO MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEP SLNEEQDKRFICKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKVVLPENLEYTIVITPHSGEEHAVGNDTGKHGK EIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMEDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKIVKEIAETQHGTI VIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQ MFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVSLV LVGVVTLYLGVMVQA B1PP76 D14.F25.S02 Fab light chain Homo sapiens 0.011679897 2 Cricetulus griseus LEVO QSALTQPRSVSGSPGQSVTISCTGTSSDVGGYKYVSWYQQHPGKAPKLMIYDVTKRPSGVPDRFSGSKSGNTASLTISGL QADDEADYYCCSYAGSYTHVVFGGGTKLTVL D14.F25.S02 Fab heavy chain Homo sapiens 0.013980643 2 Cricetulus griseus LEVO QVQLVQSGAEVKKPGSSAKVSCKASGGTFSSYAISWVRQAPGQGLEWMGSIMPIFGTVNYAQKFQGRVTITADESTSTAY MELSRLRSEDTAVYFCARGWGGNYRSADLWIYFDLWGQGTLVTVSSRS Membrane glycoprotein dengue virus type 2 DENV-2/US/BID-V594/2006 0.008373814 3 LEVO SVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQRALIFILLTAVAPSMT B1PP76 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 6 NAG singleParticle 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 ETHANE 90 277 LEICA EM GP
GP2.
DENV2 virus in complex with D14.F25.S02 Fab
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 1 18787 40.0
Images were collected in counting mode and dose fractionated into 38 frames.
 1 46826 cryoSPARC 4.6.0 PHASE FLIPPING AND AMPLITUDE CORRECTION
sphere
 1 I FOURIER SPACE 4.09 FSC 0.143 CUT-OFF cryoSPARC 4.6.0 2305 MAXIMUM LIKELIHOOD cryoSPARC 4.6.0 MAXIMUM LIKELIHOOD cryoSPARC 4.6.0 4 2000.0 cryoSPARC 4.6.0 emd_63643.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 800 800 800 0 0 0 800 800 800 880.0 880.0 880.0 90.0 90.0 90.0 Z Y X -0.13059361 0.3329047 0.0011628543 0.020063134 1.1 1.1 1.1 0.028 AUTHOR Cryo-EM map of DENV2-US/BID-V594/2006 in complex with D14.F25.S02 Fab Other in silico model
For DENV2 E and M protein
 AlphaFold in silico model
For D14.F25.S02 fab
 RIGID BODY FIT UCSF Chimera 1.17
E-protein model was built using EMProt and Fab model was predicted from Alphafold. Realspace refined model from high resolution focused map was taken for rigid body. Map to model correlation is 0.84.
REAL emd_63643_msk_1.map emd_63643_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 800 800 800 0 0 0 800 800 800 880.0 880.0 880.0 90.0 90.0 90.0 X Y Z -1.1345204 0.9210997 0.0026770069 0.12043124 1.1 1.1 1.1 AUTHOR Cryo-EM half map of DENV2-US/BID-V594/2006 in complex with D14.F25.S02 Fab emd_63643_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 800 800 800 0 0 0 800 800 800 880.0 880.0 880.0 90.0 90.0 90.0 X Y Z -0.9465178 0.95026135 0.0025975243 0.118807234 1.1 1.1 1.1 AUTHOR Cryo-EM half map of DENV2-US/BID-V594/2006 in complex with D14.F25.S02 Fab