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- EMDB-37252: Structure of tomato spotted wilt virus L protein binding to Ribavirin -

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Basic information

Entry
Database: EMDB / ID: EMD-37252
TitleStructure of tomato spotted wilt virus L protein binding to Ribavirin
Map data
Sample
  • Complex: Structure of tomato spotted wilt virus L protein binding to Ribavirin
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide
Keywordstomato spotted wilt virus / L protein / VIRAL PROTEIN
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent 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: 3.4 Å
AuthorsCao L / Wang X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: structure of tomato spotted wilt virus L protein
Authors: Cao L / Wang X
History
DepositionAug 23, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37252.png

Downloads & links

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Map

FileDownload / File: emd_37252.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: 0.38
Minimum - Maximum-2.516798 - 3.801608
Average (Standard dev.)0.00022892185 (±0.086050496)
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 Ribavirin

EntireName: Structure of tomato spotted wilt virus L protein binding to Ribavirin
Components
  • Complex: Structure of tomato spotted wilt virus L protein binding to Ribavirin
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide

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Supramolecule #1: Structure of tomato spotted wilt virus L protein binding to Ribavirin

SupramoleculeName: Structure of tomato spotted wilt virus L protein binding to Ribavirin
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: 204.262906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda multiple nucleopolyhedrovirus
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: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide

MacromoleculeName: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide
type: ligand / ID: 2 / Number of copies: 2 / Formula: RBV
Molecular weightTheoretical: 244.205 Da
Chemical component information

ChemComp-RBV:
1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide / medication, antivirus*YM

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 348921
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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