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- EMDB-61241: TSWV L protein in complex with ribavirin 5-triphosphate -

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Basic information

Entry
Database: EMDB / ID: EMD-61241
TitleTSWV L protein in complex with ribavirin 5-triphosphate
Map data
Sample
  • Complex: TSWV L protein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: RIBAVIRIN TRIPHOSPHATE
KeywordsTSWV / L protein / ribavirin 5-triphosphate / VIRAL PROTEIN
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription
Similarity search - Function
RNA-directed RNA polymerase, tospovirus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthotospovirus tomatomaculae
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCao L / Wang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
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 21, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61241.png

Downloads & links

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Map

FileDownload / File: emd_61241.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.34288532 - 0.7970521
Average (Standard dev.)0.00064785866 (±0.027107313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61241_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61241_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : TSWV L protein

EntireName: TSWV L protein
Components
  • Complex: TSWV L protein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: RIBAVIRIN TRIPHOSPHATE

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Supramolecule #1: TSWV L protein

SupramoleculeName: TSWV L protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Orthotospovirus tomatomaculae

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Orthotospovirus tomatomaculae
Molecular weightTheoretical: 203.180734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FFSHWTSKYK ERNPTEIAYS EDIERIIDSL VTDEITKEEI IHFLFGNFCF HIETMNDQHI ADKFKGYQSS CINLKIEPKV DLADLKDHL IQKQQIWESL YGKHLEKIML RIREKKKKEK EIPDITTAFN QNAAEYEEKY PNCFTNDLSE TKTNFSMTWS P SFEKIELS ...String:
FFSHWTSKYK ERNPTEIAYS EDIERIIDSL VTDEITKEEI IHFLFGNFCF HIETMNDQHI ADKFKGYQSS CINLKIEPKV DLADLKDHL IQKQQIWESL YGKHLEKIML RIREKKKKEK EIPDITTAFN QNAAEYEEKY PNCFTNDLSE TKTNFSMTWS P SFEKIELS SEVDYNNAII NKFRESFKSS SRVIYNSPYS SINNQTNKAR DITNLVRLCL TELSCDTTKM EKQELEDEID IN TGSIKVE RTKKSKEWNK QGSCLTRNKN EFCMKETGRE NKTIYFKGLA VMNIGMSSKK RILKKEEIKE RISKGLEYDT SER QADPND DYSSIDMSSL THMKKLIRHD NEDSLSWCER IKDSLFVLHN GDIREEGKIT SVYNNYAKNP ECLYIQDSVL KTEL ETCKK INKLCNDLAI YHYSEDMMQF SKGLMVADRY MTKESFKILT TANTSMMLLA FKGDGMNTGG SGVPYIALHI VDEDM SDQF NICYTKEIYS YFRNGSNYIY IMRPQRLNQV RLLSLFKTPS KVPVCFAQFS KKANEMEKWL KNKDIEKVNV FSMTMT VKQ ILINIVFSSV MIGTVTKLSR MGIFDFMRYA GFLPLSDYSN IKEYIRDKFD PDITNVADIY FVNGIKKLLF RMEDLNL ST NAKPVVVDHE NDIIGGITDL NIKCPITGST LLTLEDLYNN VYLAIYMMPK SLHNHVHNLT SLLNVPAEWE LKFRKELG F NIFEDIYPKK AMFDDKDLFS INGALNVKAL SDYYLGNIEN VGLMRSEIEN KEDFLSPCYK ISTLKSSKKC SQSNIISTD EIIECLQNAK IQDIENWKGN NLAIIKGLIR TYNEEKNRLV EFFEDNCVNS LYLVEKLKEI INSGSITVGK SVTSKFIRNN HPLTVETYL KTKLYYRNNV TVLKSKKVSE ELYDLVKQFH NMMEIDLDSV MNLGKGTEGK KHTFLQMLEF VMSKAKNVTG S VDFLVSVF EKMQRTKTDR EIYLMSMKVK MMLYFIEHTF KHVAQSDPSE AISISGDNKI RALSTLSLDT ITSYNDILNK NS KKSRLAF LSADQSKWSA SDLTYKYVLA IILNPILTTG EASLMIECIL MYVKLKKVCI PTDIFLNLRK AQGTFGQNET AIG LLTKGL TTNTYPVSMN WLQGNLNYLS SVYHSCAMKA YHKTLECYKD CDFQTRWIVH SDDNATSLIA SGEVDKMLTD FSSS SLPEM LFRSIEAHFK SFCITLNPKK SYASSSEVEF ISERIVNGAI IPLYCRHLAN CCTESSHISY FDDLMSLSIH VTMLL RKGC PNEVIPFAYG AVQVQALSIY SMLPGEVNDS IRIFKKLGVS LKSNEIPTNM GGWLTSPIEP LSILGPSSND QIIYYN VIR DFLNKKSLEE VKDSVSSSSY LQMRFRELKG KYEKGTLEEK DKKMIFLINL FEKASVSEDS DVLTIGMKFQ TMLTQII KL PNFINENALN KMSSYKDFSK LYPNLKKNED LYKSTAKNLK IDEDAILEED ELYEKIASSL EMESVHDIMI KNPETILI A PLNDRDFLLS QLFMYTSPSK RNQLSNQSTA KLALDRVLRS KARTFVDISS TEKMTYEENM EKKILEMLKF DLDSYCSFK TCVNLVIKDV NFSMLIPILD SAYPCESRKR DNYNFRWFQT EKWIPVVEGS PGLVVMHAVY GSNYIENLGL KNIPLTDDSI NVLTSTFGT GLIMEDVKSL VKGKDSFETE AFSNSNECQR LVKACNYMIA AQNRLLAINT CFTRKSFPFY SKFNLGRGFI S NTLALL

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: RIBAVIRIN TRIPHOSPHATE

MacromoleculeName: RIBAVIRIN TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: RTP
Molecular weightTheoretical: 484.144 Da
Chemical component information

ChemComp-RTP:
RIBAVIRIN TRIPHOSPHATE

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144209
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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