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- EMDB-37254: structure of Tomato spotted wilt virus L protein binding to 5'vRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-37254
Titlestructure of Tomato spotted wilt virus L protein binding to 5'vRNA
Map data
Sample
  • Complex: structure of Tomato spotted wilt virus L protein binding to 5'vRNA
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3')
KeywordsTomato spotted wilt virus / L protein / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
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 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCao L / Wang X
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) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_37254.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.53
Minimum - Maximum-3.118959 - 5.092358
Average (Standard dev.)0.00020735296 (±0.10856813)
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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Sample components

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Entire : structure of Tomato spotted wilt virus L protein binding to 5'vRNA

EntireName: structure of Tomato spotted wilt virus L protein binding to 5'vRNA
Components
  • Complex: structure of Tomato spotted wilt virus L protein binding to 5'vRNA
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3')

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Supramolecule #1: structure of Tomato spotted wilt virus L protein binding to 5'vRNA

SupramoleculeName: structure of Tomato spotted wilt virus L protein binding to 5'vRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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
Source (natural)Organism: Orthotospovirus tomatomaculae
Molecular weightTheoretical: 204.262906 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 SSINNQTNKA RDITNLVRLC LTELSCDTTK MEKQELEDEI DI NTGSIKV ERTKKSKEWN KQGSCLTRNK NEFCMKETGR ENKTIYFKGL AVMNIGMSSK KRILKKEEIK ERISKGLEYD TSE RQADPN DDYSSIDMSS LTHMKKLIRH DNEDSLSWCE RIKDSLFVLH NGDIREEGKI TSVYNNYAKN PECLYIQDSV LKTE LETCK KINKLCNDLA IYHYSEDMMQ FSKGLMVADR YMTKESFKIL TTANTSMMLL AFKGDGMNTG GSGVPYIALH IVDED MSDQ FNICYTKEIY SYFRNGSNYI YIMRPQRLNQ VRLLSLFKTP SKVPVCFAQF SKKANEMEKW LKNKDIEKVN VFSMTM TVK QILINIVFSS VMIGTVTKLS RMGIFDFMRY AGFLPLSDYS NIKEYIRDKF DPDITNVADI YFVNGIKKLL FRMEDLN LS TNAKPVVVDH ENDIIGGITD LNIKCPITGS TLLTLEDLYN NVYLAIYMMP KSLHNHVHNL TSLLNVPAEW ELKFRKEL G FNIFEDIYPK KAMFDDKDLF SINGALNVKA LSDYYLGNIE NVGLMRSEIE NKEDFLSPCY KISTLKSSKK CSQSNIIST DEIIECLQNA KIQDIENWKG NNLAIIKGLI RTYNEEKNRL VEFFEDNCVN SLYLVEKLKE IINSGSITVG KSVTSKFIRN NHPLTVETY LKTKLYYRNN VTVLKSKKVS EELYDLVKQF HNMMEIDLDS VMNLGKGTEG KKHTFLQMLE FVMSKAKNVT G SVDFLVSV FEKMQRTKTD REIYLMSMKV KMMLYFIEHT FKHVAQSDPS EAISISGDNK IRALSTLSLD TITSYNDILN KN SKKSRLA FLSADQSKWS ASDLTYKYVL AIILNPILTT GEASLMIECI LMYVKLKKVC IPTDIFLNLR KAQGTFGQNE TAI GLLTKG LTTNTYPVSM NWLQGNLNYL SSVYHSCAMK AYHKTLECYK DCDFQTRWIV HSDDNATSLI ASGEVDKMLT DFSS SSLPE MLFRSIEAHF KSFCITLNPK KSYASSSEVE FISERIVNGA IIPLYCRHLA NCCTESSHIS YFDDLMSLSI HVTML LRKG CPNEVIPFAY GAVQVQALSI YSMLPGEVND SIRIFKKLGV SLKSNEIPTN MGGWLTSPIE PLSILGPSSN DQIIYY NVI RDFLNKKSLE EVKDSVSSSS YLQMRFRELK GKYEKGTLEE KDKKMIFLIN LFEKASVSED SDVLTIGMKF QTMLTQI IK LPNFINENAL NKMSSYKDFS KLYPNLKKNE DLYKSTKNLK IDEDAILEED ELYEKIASSL EMESVHDIMI KNPETILI A PLNDRDFLLS QLFMYTSPSK RNQLSNQSTE KLALDRVLRS KARTFVDISS TVKMTYEENM EKKILEMLKF DLDSYCSFK TCVNLVIKDV NFSMLIPILD SAYPCESRKR DNYNFRWFQT EKWIPVVEGS PGLVVMHAVY GSNYIENLGL KNIPLTDDSI NVLTSTFGT GLIMEDVKSL VKGKDSFETE AFSNSNECQR LVKACNYMIA AQNRLLAINT CFTRKSFPFY SKFNLGRGFI S NTLALLST IYSKEES

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.208012 KDa
SequenceString:
AGAGCAAUCA

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 546131
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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