2026-06-24 REL PDBe PDBe PDBe 2024-01-24 2024-12-04 2024-12-04 2026-06-24 Other government 675879 Italy N.meningitidis NadV3 surface expressed homotrimeric antigen structure Calvaresi V Dello Iacono L Borghi S Luzzi E Biolchi A Benucci B Ferlenghi I Peschiera I Giusti F Fontana LE Kan Z Spinello Z Merola M Delany I Rand KD Norris N structural vaccinology, bacterial antigen, autotransporter, CELL ADHESION Calvaresi V Dello Iacono L Borghi S Luzzi E Biolchi A Ferlenghi I Peschiera I Giusti F Fontana LE Kan ZY Spinello Z Merola M Delany I Rand KD Norais N Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA. Nat Commun UK 17 2026 41807399 doi:10.1038/s41467-026-70059-1 2041-1723 PDB 6EUN unspecified
6EUN contains the coordinates of the same homotrimer obtained by Cryo-EM
 EMDB EMD-19474 associated EM volume homotrimeric coiled-coil FL NadA bacterial adhesin expressed on the surface of bacteria N.meningitidis homotrimeric coiled-coil FL NadA bacterial adhesin expressed on the surface of bacteria N.meningitidis 0 1
NadAV3 appendage generated
Neisseria meningitidis B NadAV3 Neisseria meningitidis serogroup B DDVKKAATVAIAAAYNNGQEINGFKAGETIYDIDEDGTITKKDATAADVE ADDFKGLGLKKVVTNLTKTVNENKQNVDAKVKAAESEIEKLTTKLADTDA ALADTDAALDATTNALNKLGENITTFAEETKTNIVKIDEKLEAASKHDDV KKAATVAIAAAYNNGQEINGFKAGETIYDIDEDGTITKKDATAADVEADD FKGLGLKKVVTNLTKTVNENKQNVDAKVKAAESEIEKLTTKLADTDAALA DTDAALDATTNALNKLGENITTFAEETKTNIVKIDEKLEAASDDVKKAAT VAIAAAYNNGQEINGFKAGETIYDIDEDGTITKKDATAADVEADDFKGLG LKKVVTNLTKTVNENKQNVDAKVKAAESEIEKLTTKLADTDAALADTDAA LDATTNALNKLGENITTFAEETKTNIVKIDEKLEAAS other Escherichia coli singleParticle filament 1.00 7.0 20.0 tris-HCL Tris-HCL 150.0 NaCl sodium chloride
20 mM Tris-HCL, 150 mM NaCl
 EMS Lacey Carbon COPPER 400 CARBON HOLEY 1.0 GLOW DISCHARGE AIR
Quantifoil R2-2 grid, 400 mesh Cu, Electron Microscopy Sciences) was rendered hydrophilic with 15 mA current for 90 second by glow discharge in a EmiTech K100X
 ETHANE 100 277.15 FEI VITROBOT MARK IV
Quantifoil R2-2 grid, 400 mesh Cu, Electron Microscopy Sciences) charged with 2.5 microliter of the specimens were deposited onto the grid and vitrified using a Mark IV Vitrobot with a blotting time of 4 second and humidity of 100 at 277.15K.
the sample was homogeneously distributed, no aggregation was observed. Original 1mg/ml NadAV3 sample was diluted up to 0.067 mg/ml for further EMM observations.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.4 2.0 FEI FALCON III (4k x 4k) 100.0 1 15273 NONE 14.2 FSC 0.143 CUT-OFF Xmipp
the image processing has been performed within Scipion Software platform. The particles were classified several times to prune the set in 2D using Relion. Best classes obtained were used to generate an initial model within EMAN2.
7327 NOT APPLICABLE NOT APPLICABLE emd_19474.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 420.0 420.0 420.0 90.0 90.0 90.0 X Y Z -0.015418739 0.12839699 0.00006227523 0.0034690902 1.75 1.75 1.75 0.00741 AUTHOR N.meningitidis NadAV3 homotrimeric map 6EUN 24-170 PDB experimental model
the initial model consisted of the complete biological assembly for PDB entry 6EUN
 RIGID BODY FIT
rigid-body fitting was done using ChimeraX. The position of rigid body fitted PDB 6EUN coordinates into the 3DEM map has been saved.Image of the rigid body fitting has been uploaded.
cross-correlation coefficient REAL 0.4796 emd_19474_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 420.0 420.0 420.0 90.0 90.0 90.0 X Y Z -0.016851837 0.12864643 0.00007626918 0.0032554858 1.75 1.75 1.75 AUTHOR half1 map for FSC emd_19474_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 420.0 420.0 420.0 90.0 90.0 90.0 X Y Z -0.017251864 0.12805815 0.00007846441 0.0032615701 1.75 1.75 1.75 AUTHOR helf2 map for FSC