Structure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein

2026-10-07 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-11-04 2026-10-07 2026-10-07 2026-10-07 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R37 AI059371 United States Agence Nationale de la Recherche (ANR) ANR-23-CE11-0001-01 France Structure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein Bloyet LM Whelan SPJ Vesicular stomatitis virus, L protein, P protein, phosphoprotein, nucleoprotein, N protein, single particle analysis, replication, virus, protein complex, N0-P complex, replication complex, VIRAL PROTEIN Bloyet LM Whelan SPJ Structure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein To Be Published 0353 9t53 FULLOVERLAP EMDB EMD-55567 associated EM volume

VSIV L:P:N complex VSIV L:P:N complex 0 1 2 3

L protein (full-length) in complex with P protein (1-106) and N protein (full-length)

Vesicular stomatitis Indiana virus strain San Juan 0.05 L:P complex 1 1 3

L protein (full-length) in complex with a fragment of P (49-106)

Vesicular stomatitis Indiana virus strain San Juan N0-P complex 1 2 3

N protein (full-length) in complex with a framgent of P (5-32)

Vesicular stomatitis Indiana virus strain San Juan RNA-directed RNA polymerase L Vesicular stomatitis Indiana virus strain San Juan 0.24133992199999998 1 Mesocricetus auratus LEVO GPMEVHDFETDEFNDFNEDDYATREFLNPDERMTYLNHADYNLNSPLISDDIDNLIRKFNSLPIPSMWDSKNWDGVLEML TSCQANPISTSQMHKWMGSWLMSDNHDASQGYSFLHEVDKEAEITFDVVETFIRGWGNKPIEYIKKERWTDSFKILAYLC QKFLDLHKLTLILNAVSEVELLNLARTFKGKVRRSSHGTNICRIRVPSLGPTFISEGWAYFKKLDILMDRNFLLMVKDVI IGRMQTVLSMVCRIDNLFSEQDIFSLLNIYRIGDKIVERQGNFSYDLIKMVEPICNLKLMKLARESRPLVPQFPHFENHI KTSVDEGAKIDRGIRFLHDQIMSVKTVDLTLVIYGSFRHWGHPFIDYYTGLEKLHSQVTMKKDIDVSYAKALASDLARIV LFQQFNDHKKWFVNGDLLPHDHPFKSHVKENTWPTAAQVQDFGDKWHELPLIKCFEIPDLLDPSIIYSDKSHSMNRSEVL KHVRMNPNTPIPSKKVLQTMLDTKATNWKEFLKEIDEKGLDDDDLIIGLKGKERELKLAGRFFSLMSWKLREYFVITEYL IKTHFVPMFKGLTMADDLTAVIKKMLDSSSGQGLKSYEAICIANHIDYEKWNNHQRKLSNGPVFRVMGQFLGYPSLIERT HEFFEKSLIYYNGRPDLMRVHNNTLINSTSQRVCWQGQEGGLEGLRQKGWSILNLLVIQREAKIRNTAVKVLAQGDNQVI CTQYKTKKSRNVVELQGALNQMVSNNEKIMTAIKIGTGKLGLLINDDETMQSADYLNYGKIPIFRGVIRGLETKRWSRVT CVTNDQIPTCANIMSSVSTNALTVAHFAENPINAMIQYNYFGTFARLLLMMHDPALRQSLYEVQDKIPGLHSSTFKYAML YLDPSIGGVSGMSLSRFLIRAFPDPVTESLSFWRFIHVHARSEHLKEMSAVFGNPEIAKFRITHIDKLVEDPTSLNIAMG MSPANLLKTEVKKCLIESRQTIRNQVIKDATIYLYHEEDRLRSFLWSINPLFPRFLSEFKSGTFLGVADGLISLFQNSRT IRNSFKKKYHRELDDLIVRSEVSSLTHLGKLHLRRGSCKMWTCSATHADTLRYKSWGRTVIGTTVPHPLEMLGPQHRKET PCAPCNTSGFNYVSVHCPDGIHDVFSSRGPLPAYLGSKTSESTSILQPWERESKVPLIKRATRLRDAISWFVEPDSKLAM TILSNIHSLTGEEWTKRQHGFKRTGSALHRFSTSRMSHGGFASQSTAALTRLMATTDTMRDLGDQNFDFLFQATLLYAQI TTTVARDGWITSCTDHYHIACKSCLRPIEEITLDSSMDYTPPDVSHVLKTWRNGEGSWGQEIKQIYPLEGNWKNLAPAEQ SYQVGRCIGFLYGDLAYRKSTHAEDSSLFPLSIQGRIRGRGFLKGLLDGLMRASCCQVIHRRSLAHLKRPANAVYGGLIY LIDKLSVSPPFLSLTRSGPIRDELETIPHKIPTSYPTSNRDMGVIVRNYFKYQCRLIEKGKYRSHYSQLWLFSDVLSIDF IGPFSISTTLLQILYKPFLSGKDKNELRELANLSSLLRSGEGWEDIHVKFFTKDILLCPEEIRHACKFGIAKDNNKDMSY PPWGRESRGTITTIPVYYTTTPYPKMLEMPPRIQNPLLSGIRLGQLPTGAHYKIRSILHGMGIHYRDFLSCGDGSGGMTA ALLRENVHSRGIFNSLLELSGSVMRGASPEPPSALETLGGDKSRCVNGETCWEYPSDLCDPRTWDYFLRLKAGLGLQIDL IVMDMEVRDSSTSLKIETNVRNYVHRILDEQGVLIYKTYGTYICESEKNAVTILGPMFKTVDLVQTEFSSSQTSEVYMVC KGLKKLIDEPNPDWSSINESWKNLYAFQSSEQEFARAKKVSTYFTLTGIPSQFIPDPFVNIETMLQIFGVPTGVSHAAAL KSSDRPADLLTISLFYMAIISYYNINHIRVGPIPPNPPSDGIAQNVGIAITGISFWLSLMEKDIPLYQQCLAVIQQSFPI RWEAISVKGGYKQKWSTRGDGLPKDTRISDSLAPIGNWIRSLELVRNQVRLNPFNKILFNQLCRTVDNHLKWSNLRKNTG MIEWINGRISKEDRSILMLKSDLHEENSWRD P03523 2.7.7.48 Nucleoprotein Vesicular stomatitis Indiana virus strain San Juan 0.047463949 1 Escherichia coli BL21(DE3) LEVO MSVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINTTKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDI RGKLDKDWSSFGINIGKAGDTIGIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKKLMDGL TNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTIVSRFKDCAALATFGHLCKITGM STEDVTTWILNREVADEMVQMMLPGQEIDKADSYMPYLIDFGLSSKSPYSSVKNPAFHFWGQLTALLLRSTRARNARQPD DIEYTSLTTAGLLYAYAVGSSADLAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPDMMQYAKRA VMSLQGLREKTIGKYAKSEFDK P03521 Phosphoprotein Vesicular stomatitis Indiana virus strain San Juan 0.013054788 1 Escherichia coli BL21(DE3) LEVO MDNLTKVREYLKSYSRLDQAVGEIDEIEAQRAEKSNYELFQEDGVEEHTRPSYFQAADDSDTESEPEIEDNQGLYVPDPE AEQVEGFIQGPLDDYADEDVDVVFTSGSGLEVLFQ P03520 ZINC ION 6.5409e-05 2 ZN singleParticle particle 8.0 PELCO Ultrathin Carbon with Lacey Carbon COPPER 300 CARBON LACEY GLOW DISCHARGE 15 ETHANE FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.8 2.4 EPU 3.5.1 FEI FALCON IV (4k x 4k) 3881 8.38 55.99 FEI FALCON IV (4k x 4k) 6441 7.27 54.38 1

Gain-corrected movies were aligned using cryoSPARC

cryoSPARC 4.6

CTF estimation and correction with cryoSPARC

PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab-initio reconstruction

3.8 FSC 0.143 CUT-OFF cryoSPARC 4.6 3D Flex

3D Flexible refinement

34000 MAXIMUM LIKELIHOOD cryoSPARC 4.6 MAXIMUM LIKELIHOOD cryoSPARC 4.6 emd_55567.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 263.2 263.2 263.2 90.0 90.0 90.0 X Y Z -0.029227572 0.060330108 0.00010343011 0.0027063766 0.94000006 0.94000006 0.94000006 0.01 AUTHOR ::::EMDATABANK.org::::EMD-55567:::: 6U1X PDB experimental model 3PMK PDB experimental model RIGID BODY FIT UCSF ChimeraX 1.9.dev202410260116

L-P from 6U1X was rigid-body fitted in the map. N0-P from 3PMK (chains D and O) was rigid-body fitted in the map after deletion of the C-loop (aa 342-374). The model was then locally edited and refined to introduce mutations and solve clashes.

Cross-correlation coefficient REAL emd_55567_msk_1.map emd_55567_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 263.2 263.2 263.2 90.0 90.0 90.0 X Y Z -0.0017673672 2.323988 0.0029082308 0.040770315 0.94000006 0.94000006 0.94000006 AUTHOR ::::EMDATABANK.org::::EMD-55567:::: Map post-processed by DeepEMhancer emd_55567_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 263.2 263.2 263.2 90.0 90.0 90.0 X Y Z -0.04886277 0.08373034 0.00010943238 0.0040653846 0.94000006 0.94000006 0.94000006 AUTHOR ::::EMDATABANK.org::::EMD-55567:::: emd_55567_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 263.2 263.2 263.2 90.0 90.0 90.0 X Y Z -0.045944266 0.08225835 0.00009742784 0.0041680685 0.94000006 0.94000006 0.94000006 AUTHOR ::::EMDATABANK.org::::EMD-55567::::