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- EMDB-37256: Tomato spotted wilt virus L protein (apo state) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37256
TitleTomato spotted wilt virus L protein (apo state)
Map data
Sample
  • Complex: Tomato spotted wilt virus Lprotein
    • Protein or peptide: RNA-directed RNA polymerase L
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: 4.0 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_37256.png

Downloads & links

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Map

FileDownload / File: emd_37256.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 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: 0.016
Minimum - Maximum-0.037838247 - 0.07116922
Average (Standard dev.)-0.0000011950425 (±0.0016292034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37256_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_37256_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tomato spotted wilt virus Lprotein

EntireName: Tomato spotted wilt virus Lprotein
Components
  • Complex: Tomato spotted wilt virus Lprotein
    • Protein or peptide: RNA-directed RNA polymerase L

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Supramolecule #1: Tomato spotted wilt virus Lprotein

SupramoleculeName: Tomato spotted wilt virus Lprotein / 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 / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Orthotospovirus tomatomaculae
Molecular weightTheoretical: 204.394062 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVFFSHWTSK YKERNPTEIA YSEDIERIID SLVTDEITKE EIIHFLFGNF CFHIETMNDQ HIADKFKGYQ SSCINLKIEP KVDLADLKD HLIQKQQIWE SLYGKHLEKI MLRIREKKKK EKEIPDITTA FNQNAAEYEE KYPNCFTNDL SETKTNFSMT W SPSFEKIE ...String:
DVFFSHWTSK YKERNPTEIA YSEDIERIID SLVTDEITKE EIIHFLFGNF CFHIETMNDQ HIADKFKGYQ SSCINLKIEP KVDLADLKD HLIQKQQIWE SLYGKHLEKI MLRIREKKKK EKEIPDITTA FNQNAAEYEE KYPNCFTNDL SETKTNFSMT W SPSFEKIE LSSEVDYNNA IINKFRESFK SSSRVIYNSP YSCINNQTNK ARDITNLVRL CLTELSCDTT KMEKQELEDE ID INTGSIK VERTKKSKEW NKQGSCLTRN KNEFCMKETG RENKTIYFKG LAVMNIGMSS KKRILKKEEI KERISKGLEY DTS ERQADP NDDYSSIDMS SLTHMKKLIR HDNEDSLSWC ERIKDSLFVL HNGDIREEGK ITSVYNNYAK NPECLYIQDS VLKT ELETC KKINKLCNDL AIYHYSEDMM QFSKGLMVAD RYMTKESFKI LTTANTSMML LAFKGDGMNT GGSGVPYIAL HIVDE DMSD QFNICYTKEI YSYFRNGSNY IYIMRPQRLN QVRLLSLFKT PSKVPVCFAQ FSKKANEMEK WLKNKDIEKV NVFSMT MTV KQILINIVFS SVMIGTVTKL SRMGIFDFMR YAGFLPLSDY SNIKEYIRDK FDPDITNVAD IYFVNGIKKL LFRMEDL NL STNAKPVVVD HENDIIGGIT DLNIKCPITG STLLTLEDLY NNVYLAIYMM PKSLHNHVHN LTSLLNVPAE WELKFRKE L GFNIFEDIYP KKAMFDDKDL FSINGALNVK ALSDYYLGNI ENVGLMRSEI ENKEDFLSPC YKISTLKSSK KCSQSNIIS TDEIIECLQN AKIQDIENWK GNNLAIIKGL IRTYNEEKNR LVEFFEDNCV NSLYLVEKLK EIINSGSITV GKSVTSKFIR NNHPLTVET YLKTKLYYRN NVTVLKSKKV SEELYDLVKQ FHNMMEIDLD SVMNLGKGTE GKKHTFLQML EFVMSKAKNV T GSVDFLVS VFEKMQRTKT DREIYLMSMK VKMMLYFIEH TFKHVAQSDP SEAISISGDN KIRALSTLSL DTITSYNDIL NK NSKKSRL AFLSADQSKW SASDLTYKYV LAIILNPILT TGEASLMIEC ILMYVKLKKV CIPTDIFLNL RKAQGTFGQN ETA IGLLTK GLTTNTYPVS MNWLQGNLNY LSSVYHSCAM KAYHKTLECY KDCDFQTRWI VHSDDNATSL IASGEVDKML TDFS SSSLP EMLFRSIEAH FKSFCITLNP KKSYASSSEV EFISERIVNG AIIPLYCRHL ANCCTESSHI SYFDDLMSLS IHVTM LLRK GCPNEVIPFA YGAVQVQALS IYSMLPGEVN DSIRIFKKLG VSLKSNEIPT NMGGWLTSPI EPLSILGPSS NDQIIY YNV IRDFLNKKSL EEVKDSVSSS SYLQMRFREL KGKYEKGTLE EKDKKMIFLI NLFEKASVSE DSDVLTIGMK FQTMLTQ II KLPNFINENA LNKMSSYKDF SKLYPNLKKN EDLYKSTKNL KIDEDAILEE DELYEKIASS LEMESVHDIM IKNPETIL I APLNDRDFLL SQLFMYTSPS KRNQLSNQST EKLALDRVLR SKARTFVDIS STVKMTYEEN MEKKILEMLK FDLDSYCSF KTCVNLVIKD VNFSMLIPIL DSAYPCESRK RDNYNFRWFQ TEKWIPVVEG SPGLVVMHAV YGSNYIENLG LKNIPLTDDS INVLTSTFG TGLIMEDVKS LVKGKDSFET EAFSNSNECQ RLVKACNYMI AAQNRLLAIN TCFTRKSFPF YSKFNLGRGF I SNTLALLS TIYSKEES

UniProtKB: RNA-directed RNA polymerase 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: 359068
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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