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- EMDB-37255: Structure of Tomato spotted wilt virus L protein contained CTD -

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Basic information

Entry
Database: EMDB / ID: EMD-37255
TitleStructure of Tomato spotted wilt virus L protein contained CTD
Map data
Sample
  • Complex: Tomato spotted wilt virus L protein
    • Protein or peptide: L protein
KeywordsTomato spotted wilt virus / L protein / VIRAL PROTEIN
Biological speciesOrthotospovirus tomatomaculae
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsCao L / Wang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Plants / Year: 2025
Title: Structural basis for the activation of plant bunyavirus replication machinery and its dual-targeted inhibition by ribavirin.
Authors: Jia Li / Lei Cao / Yaqian Zhao / Jinghan Shen / Lei Wang / Mingfeng Feng / Min Zhu / Yonghao Ye / Richard Kormelink / Xiaorong Tao / Xiangxi Wang /
Abstract: Despite the discovery of plant viruses as a new class of pathogens over a century ago, the structure of plant virus replication machinery and antiviral pesticide remains lacking. Here we report five ...Despite the discovery of plant viruses as a new class of pathogens over a century ago, the structure of plant virus replication machinery and antiviral pesticide remains lacking. Here we report five cryogenic electron microscopy structures of a ~330-kDa RNA-dependent RNA polymerase (RdRp) from a devastating plant bunyavirus, tomato spotted wilt orthotospovirus (TSWV), including the apo, viral-RNA-bound, base analogue ribavirin-bound and ribavirin-triphosphate-bound states. They reveal that a flexible loop of RdRp's motif F functions as 'sensor' to perceive viral RNA and further acts as an 'adaptor' to promote the formation of a complete catalytic centre. A ten-base RNA 'hook' structure is sufficient to trigger major conformational changes and activate RdRp. Chemical screening showed that ribavirin is effective against TSWV, and structural data revealed that ribavirin disrupts both hook-binding and catalytic core formation, locking polymerase in its inactive state. This work provides structural insights into the mechanisms of plant bunyavirus RdRp activation and its dual-targeted site inhibition, facilitating the development of pesticides against plant viruses.
History
DepositionAug 23, 2023-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37255.png

Downloads & links

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Map

FileDownload / File: emd_37255.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.087
Minimum - Maximum-0.0018141619 - 2.2904856
Average (Standard dev.)0.0025887846 (±0.036004175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37255_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_37255_half_map_2.map
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Sample components

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Entire : Tomato spotted wilt virus L protein

EntireName: Tomato spotted wilt virus L protein
Components
  • Complex: Tomato spotted wilt virus L protein
    • Protein or peptide: L protein

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Supramolecule #1: Tomato spotted wilt virus L protein

SupramoleculeName: Tomato spotted wilt virus L protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Orthotospovirus tomatomaculae

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Macromolecule #1: L protein

MacromoleculeName: L protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Orthotospovirus tomatomaculae
Molecular weightTheoretical: 281.912 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VFFSHWTSKY KERNPTEIAY SEDIERIIDS LVTDEITKEE IIHFLFGNFC FHIETMNDQH IADKFKGYQS SCINLKIEPK VDLADLKDH LIQKQQIWES LYGKHLEKIM LRIREKKKKE KEIPDITTAF NQNAAEYEEK YPNCFTNDLS ETKTNFSMTW S PSFEKIEL ...String:
VFFSHWTSKY KERNPTEIAY SEDIERIIDS LVTDEITKEE IIHFLFGNFC FHIETMNDQH IADKFKGYQS SCINLKIEPK VDLADLKDH LIQKQQIWES LYGKHLEKIM LRIREKKKKE KEIPDITTAF NQNAAEYEEK YPNCFTNDLS ETKTNFSMTW S PSFEKIEL SSEVDYNNAI INKFRESFKS SSRVIYNSPY STNKARDITN LVRLCLTELS CLTRNKNEFC MKETGRENKT IY FKGLAVM NIHMKKLIRH DNEDSLSWCE RIKDSLFVLH NGDIREEGKI TSVYNNYAKN PECLYIQDSV LKTELETCKK INK LCNDLA IYHYSEDMMQ FSKGLMVADR YMTKESFKIL TTANTSMMLL AFKSGVPYIA LHIVDEDMSD QFNICYTKEI YSYF RNGSN YIYIMRPQRL NQVRLLSLFK TPSKVPVCFA QFSKKANEME KWLKNKDIEK VNVFSMTMTV KQILINIVFS SVMIG TVTK LSRMGIFDFM RYAGFLPLSD YSNIKEYIRD KFDPDITNVA DIYFVNGIKK LLFRMEDLDI IGGITDLNIK CPITGS TLL TLEDLYNNVY LAIYMMPKSL HNHVHNLTSL LNVPAEWELK FRKELGFNIF EDIYPKKAMF DDKDLFSING ALNVKAL SD YYLGNIENVG LMRSEIENKE DFLSPCYKIS TLKSSKKCSQ SNIISTDEII ECLQNAKIQD IENWKGNNLA IIKGLIRT Y NEEKNRLVEF FEDNCVNSLY LVEKLKEIIN SGSITVGKSV TSKFIRNNHP LTVETYLKTK LYYRNNVTVL KSKKVSEEL YDLVKQFHNM MEIDLDSVMN LGKGTEGKKH TFLQMLEFVM SKAKNVTGSV DFLVSVYLMS MKVKMMLYFI EHTFKHVAQS DPSEAISIS GDNKIRALST LSLDTITSYN DILNKNSKKS RLAFLSADQS KWSASDLTYK YVLAIILNPI LTTGEASLMI E CILMYVKL KKVCIPTDIF LNLRKAQGTF GQNETAIGLL TKGLTTNTYP VSMNWLQGNL NYLSSVYHSC AMKAYHKTLE CY KDCDFQT RWIVHSDDNA TSLIASGEVD KMLTDFSSSS LPEMLFRSIE AHFKSFCITL NPKKSYASSS EVEFISERIV NGA IIPLYC RHLANCCTES SHISYFDDLM SLSIHVTMLL RKGCPNEVIP FAYGAVQVQA LSIYSMLPGE VNDSIRIFKK LGVS LKSNE IPTNMGGWLT SPIEPLSILG PSSNDQIIYY NVIRDFLNKK SLEEVKDSVS SSSYLQMRFR ELKGKYEKGT LEEKD KKMI FLINLFEKAT MLTQIIKLPN FINENALNKM SSYKDFSKLY PNLKKNIASS LEMESVHDIM IKNPETILIA PLNDRD FLL SQLFMYTSPS KRNQLSNQST EKLALDRVLR SKARTKMTYE ENMEKKILEM LKFDLDSYCS FKTCVNLVIK DVNFSML IP ILDSAYPCES RKRDNYNFRW FQTEKWIPVV EGSPGLVVMH AVYGSNYIEN LGLKNIPLTD DSINVLTSTF GTGLIMED Y CSFKTCVNLV IKDVNFSMLI PILDSAYPCE SRKRDNYNFR WFQTEKWIPV VEGSPGLVVM HAVYGSNYIE NLGLKNIPL TDDSINVLTS TFGTGLIMED VKSLVKGKDS FETEAFSNSN ECQRLVKACN YMIAAQNRLL AINTCFTRKS FPFYSKFNLG RGFISNTLA LLSTIYSKEE SYHFVSTASY KLDKTIRTVV SAQQDMNLEK ILDTAVYISD KLQSLFPTIT REDIVLILQN V CLDSKPIW QSLEDKMKKI NNSTASGFTV SNVILSHNSE LNTIQKQIVW MWNMGLCSHR TLDFVIRYIR RRDVRYVKTE EQ DESGNYV SGTMYKIGIM TRSCYVELIA SDQDVAVSLR TPFEILNERE YLFDTYRESI EKLLAEIMFD KVNIINQTTT DCF LRTRRS CIRMTTDNKM IVKVNATSRQ IRLENVKLVV KIKYENVDVW DIIESQKSTI KTIKNRLMTS LTFIEAFGNL SQQI KEIVD DDIRETMDEF LMNIRDTCLE GLENCKSVEE YDSYLDENGF NDTVELFENL LRTHDNFENE YSPLFSEIVD KAKQY TRDL EGFKEILLML KYSLINDASK SYRATGMHAV ELMAKKHIEI GEFNLLGMIQ LIKACETCHN NDSILNLASL RNVLSR TYA TFGRRIRLDH DLDLQNNLME KSYDFKTLVL PEIKLSELSR EILKENGFVI SGENLKMDRS DEEFVGLASF NVLRLDE EE MYEGLIKEMK IKRKKKGFLF PANTLLLSEL IKFLIGGIKG TSFDIETLLR NSFRPDIFST DRLGRLSSSV PALKVYAT V YMEYKNVNCP LNEIADSLEG YLKLTKSRSK EHFLSGRVKK ALIQLRDEQS RTKKLEVYKD IANFLARHPL CLSEKTLYG RYTYSDINDY IMQTREIILS KISELDEVVE TDEDNFLLSY L

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61445
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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