Subtomogram Average of the Nipah Virus Matrix Lattice in Complex with Human Cell Membrane inside Virus-Like-Particles

2026-08-19 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-03-13 2026-08-19 2026-08-19 2026-08-19 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI109022 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI147890-04 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI150479-09 United States Subtomogram Average of the Nipah Virus Matrix Lattice in Complex with Human Cell Membrane inside Virus-Like-Particles Upadhye VV Dick RA Assembly Lattice, VIRUS LIKE PARTICLE Upadhye VV Lee JF Ercanli N Ricana C Hinsley AC Obr M Autin L Schur FKM Aguilar HC Dick RA Cryo-electron tomography of Nipah virus structural protein complexes in virus-like particles. Biorxiv US 2026 42523209 doi:10.64898/2026.07.16.738223 2692-8205 9nqy FULLOVERLAP EMDB EMD-49696 associated EM volume

Nipah Virus Matrix Lattice in Complex with Human Cell Membrane

Henipavirus nipahense Henipavirus nipahense 0 1 Henipavirus nipahense Malaysia VIRUS-LIKE PARTICLE SPECIES true true Matrix protein Henipavirus nipahense 0.04455898 18 Homo sapiens LEVO MDYKDDDDKDYKDDDDKDYKDDDDKARAGSPGLQEFDIKLEPDIKSISSESMEGVSDFSPSSWEHGGYLDKVEPEIDENG SMIPKYKIYTPGANERKYNNYMYLICYGFVEDVERTPETGKRKKIRTIAAYPLGVGKSASHPQDLLEELCSLKVTVRRTA GSTEKIVFGSSGPLNHLVPWKKVLTSGSIFNAVKVCRNVDQIQLDKHQALRIFFLSITKLNDSGIYMIPRTMLEFRRNNA IAFNLLVYLKIDADLSKMGIQGSLDKDGFKVASFMLHLGNFVRRAGKYYSVDYCRRKIDRMKLQFSLGSIGGLSLHIKIN GVISKRLFAQMGFQKNLCFSLMDINPWLNRLTWNNSCEISRVAAVLQPSIPREFMIYDDVFIDNTGRILKG Q9IK90 subtomogramAveraging threeDArray 7.5 50.0 Tris 150.0 NaCl 1.0 EDTA Quantifoil R2/2 GOLD 300 CARBON HOLEY ARRAY GLOW DISCHARGE 45 AIR 0.039 ETHANE 100 277 LEICA EM GP FEI TALOS ARCTICA SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.5 3.5 63000.0 NITROGEN GIF Bioquantum 20

Zero Loss Peak was refined after every tilt series

GATAN K3 BIOQUANTUM (6k x 4k) 1 3.65 1 C2 7.0 FSC 0.143 CUT-OFF RELION 4.0 Tomo 9767 24 340688 Ab-initio Manually annotated Dynamo 1.1.532 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION MAXIMUM LIKELIHOOD RELION 4.0 Tomo Tomo emd_49696.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 340.59998 340.59998 340.59998 90.0 90.0 90.0 X Y Z -14.846776999999999 19.354372000000001 0.000010302783 0.7783937 1.31 1.31 1.31 3.8 AUTHOR ::::EMDATABANK.org::::EMD-49696:::: AlphaFold in silico model RIGID BODY FIT

The initial model of 1 M Dimer was generated with AlphaFold2. Model was docked into map in Chimera v1.1.4. RealSpaceRefine in Phenix of 1 M Dimer. Open refined model and map in Chimera. Duplicate model, rotate and dock. Re run RealSpaceRefine. Repeat for all dimers present in electron density map. Run comprehensive validation in Phenix which resulted in Ramachandran outliers of 0%, Allowed 7% and Favored of 93% . We then removed all side chains from model prior to PDB deposition since our map does not support any side chain density - only backbone.

CC REAL 351.0 emd_49696_msk_1.map emd_49696_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 348.4 348.4 348.4 90.0 90.0 90.0 X Y Z -15.873372 18.424288000000001 0.000000000037467 2.2185104 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::EMD-49696:::: merged unfiltered map emd_49696_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 348.4 348.4 348.4 90.0 90.0 90.0 X Y Z -23.965928999999999 23.707816999999999 -0.000000000030902 3.0867498 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::EMD-49696:::: emd_49696_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 260 260 260 0 0 0 260 260 260 348.4 348.4 348.4 90.0 90.0 90.0 X Y Z -22.803476 23.815629999999999 -0.000000000020693 3.1018066 1.34 1.34 1.34 AUTHOR ::::EMDATABANK.org::::EMD-49696::::