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- EMDB-37253: Structure of Tomato spotted wilt virus L protein contained endoH ... -

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Basic information

Entry
Database: EMDB / ID: EMD-37253
TitleStructure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'vRNA
Map data
Sample
  • Complex: Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'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')
    • RNA: RNA (5'-R(P*GP*CP*AP*AP*UP*CP*AP*GP*G)-3')
    • RNA: RNA (5'-R(P*AP*CP*CP*UP*GP*AP*UP*UP*GP*CP*UP*CP*U)-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 speciesTomato spotted wilt virus (strain Bulgarian L3) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_37253.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 220 pix.
= 228.8 Å		1.04 Å/pix.
x 220 pix.
= 228.8 Å		1.04 Å/pix.
x 220 pix.
= 228.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.9432925 - 1.5304993
Average (Standard dev.)0.0030426618 (±0.06372672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 228.79999 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 contained endoH ...

EntireName: Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'vRNA
Components
  • Complex: Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'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')
    • RNA: RNA (5'-R(P*GP*CP*AP*AP*UP*CP*AP*GP*G)-3')
    • RNA: RNA (5'-R(P*AP*CP*CP*UP*GP*AP*UP*UP*GP*CP*UP*CP*U)-3')

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Supramolecule #1: Structure of Tomato spotted wilt virus L protein contained endoH ...

SupramoleculeName: Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'vRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tomato spotted wilt virus (strain Bulgarian L3)

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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: Tomato spotted wilt virus (strain Bulgarian L3) / Strain: Bulgarian L3
Molecular weightTheoretical: 240.378375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNIQKIQKLI ENGTTLLLSI EDCVGSNYDL ALDLHKRNSD EIPEDVIINN NAKNYETMRE LIVKITADGE GLNKGMATVD VKKLSEMVS LFEQKYLETE LARHDIFGEL ISRHLRIKPK QRSEVEIEHA LREYLDELNK KSCINKLSDD EFERINKEYV A TNATPDNY ...String:
MNIQKIQKLI ENGTTLLLSI EDCVGSNYDL ALDLHKRNSD EIPEDVIINN NAKNYETMRE LIVKITADGE GLNKGMATVD VKKLSEMVS LFEQKYLETE LARHDIFGEL ISRHLRIKPK QRSEVEIEHA LREYLDELNK KSCINKLSDD EFERINKEYV A TNATPDNY VIYKESKNSE LCLIIYDWKI SVDARTETKT MEKYYKNIWK SFKDIKVNGK PFLEDHPVFV SIVILKPIAG MP ITVTSSR VLEKFEDSPS ALHGERIKHA RNAKLLNISH VGQIVGTTPT VVRNYYANTQ KIKSEVRGIL GDDFGSKDVF FSH WTSKYK ERNPTEIAYS EDIERIIDSL VTDEITKEEI IHFLFGNFCF HIETMNDQHI ADKFKGYQSS CINLKIEPKV DLAD LKDHL IQKQQIWESL YGKHLEKIML RIREKKKKEK EIPDITTAFN QNAAEYEEKY PNCFTNDLSE TKTNFSMTWS PSFEK IELS SEVDYNNAII NKFRESFKSS SRVIYNSPYS SINNQTNKAR DITNLVRLCL TELSCDTTKM EKQELEDEID INTGSI KVE RTKKSKEWNK QGSCLTRNKN EFCMKETGRE NKTIYFKGLA VMNIGMSSKK RILKKEEIKE RISKGLEYDT SERQADP ND DYSSIDMSSL THMKKLIRHD NEDSLSWCER IKDSLFVLHN GDIREEGKIT SVYNNYAKNP ECLYIQDSVL KTELETCK K INKLCNDLAI YHYSEDMMQF SKGLMVADRY MTKESFKILT TANTSMMLLA FKGDGMNTGG SGVPYIALHI VDEDMSDQF NICYTKEIYS YFRNGSNYIY IMRPQRLNQV RLLSLFKTPS KVPVCFAQFS KKANEMEKWL KNKDIEKVNV FSMTMTVKQI LINIVFSSV MIGTVTKLSR MGIFDFMRYA GFLPLSDYSN IKEYIRDKFD PDITNVADIY FVNGIKKLLF RMEDLNLSTN A KPVVVDHE NDIIGGITDL NIKCPITGST LLTLEDLYNN VYLAIYMMPK SLHNHVHNLT SLLNVPAEWE LKFRKELGFN IF EDIYPKK AMFDDKDLFS INGALNVKAL SDYYLGNIEN VGLMRSEIEN KEDFLSPCYK ISTLKSSKKC SQSNIISTDE IIE CLQNAK IQDIENWKGN NLAIIKGLIR TYNEEKNRLV EFFEDNCVNS LYLVEKLKEI INSGSITVGK SVTSKFIRNN HPLT VETYL KTKLYYRNNV TVLKSKKVSE ELYDLVKQFH NMMEIDLDSV MNLGKGTEGK KHTFLQMLEF VMSKAKNVTG SVDFL VSVF EKMQRTKTDR EIYLMSMKVK MMLYFIEHTF KHVAQSDPSE AISISGDNKI RALSTLSLDT ITSYNDILNK NSKKSR LAF LSADQSKWSA SDLTYKYVLA IILNPILTTG EASLMIECIL MYVKLKKVCI PTDIFLNLRK AQGTFGQNET AIGLLTK GL TTNTYPVSMN WLQGNLNYLS SVYHSCAMKA YHKTLECYKD CDFQTRWIVH SDDNATSLIA SGEVDKMLTD FSSSSLPE M LFRSIEAHFK SFCITLNPKK SYASSSEVEF ISERIVNGAI IPLYCRHLAN CCTESSHISY FDDLMSLSIH VTMLLRKGC PNEVIPFAYG AVQVQALSIY SMLPGEVNDS IRIFKKLGVS LKSNEIPTNM GGWLTSPIEP LSILGPSSND QIIYYNVIRD FLNKKSLEE VKDSVSSSSY LQMRFRELKG KYEKGTLEEK DKKMIFLINL FEKASVSEDS DVLTIGMKFQ TMLTQIIKLP N FINENALN KMSSYKDFSK LYPNLKKNED LYKSTKNLKI DEDAILEEDE LYEKIASSLE MESVHDIMIK NPETILIAPL ND RDFLLSQ LFMYTSPSKR NQLSNQSTEK LALDRVLRSK ARTFVDISST VKMTYEENME KKILEMLKFD LDSYCSFKTC VNL VIKDVN FSMLIPILDS AYPCESRKRD NYNFRWFQTE KWIPVVEGSP GLVVMHAVYG SNYIENLGLK NIPLTDDSIN VLTS TFGTG LIMEDVKSLV KGKDSFETEA FSNSNECQRL VKACNYMIAA QNRLLAINTC FTRKSFPFYS KFNLGRGFIS NTLAL LSTI YSKEES

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

MacromoleculeName: RNA (5'-R(P*GP*CP*AP*AP*UP*CP*AP*GP*G)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.894807 KDa
SequenceString:
GCAAUCAGG

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Macromolecule #4: RNA (5'-R(P*AP*CP*CP*UP*GP*AP*UP*UP*GP*CP*UP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*AP*CP*CP*UP*GP*AP*UP*UP*GP*CP*UP*CP*U)-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.055421 KDa
SequenceString:
ACCUGAUUGC UCU

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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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156980
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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