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- EMDB-0828: Structure of severe fever with thrombocytopenia syndrome virus L ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0828
TitleStructure of severe fever with thrombocytopenia syndrome virus L protein
Map data
Sample
  • Complex: Virus polymerase
    • Protein or peptide: RNA polymerase
  • Ligand: MAGNESIUM ION
Keywordspolymease / VIRUS / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / 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 speciesPhlebovirus WCH/97/HN/China/2011
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang P / Lou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Microbiol / Year: 2020
Title: Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation.
Authors: Panpan Wang / Lu Liu / Aijun Liu / Liming Yan / Yong He / Shu Shen / Mingxu Hu / Yu Guo / Haiguang Liu / Chuang Liu / Yinying Lu / Peiyi Wang / Fei Deng / Zihe Rao / Zhiyong Lou /
Abstract: Segmented negative-sense RNA viruses (sNSRVs) encode a single-polypeptide polymerase (L protein) or a heterotrimeric polymerase complex to cannibalize host messenger RNA cap structures serving as ...Segmented negative-sense RNA viruses (sNSRVs) encode a single-polypeptide polymerase (L protein) or a heterotrimeric polymerase complex to cannibalize host messenger RNA cap structures serving as primers of transcription, and catalyse RNA synthesis. Here, we report the full-length structure of the severe fever with thrombocytopaenia syndrome virus (SFTSV) L protein, as determined by cryogenic electron microscopy at 3.4 Å, leading to an atomic model harbouring three functional parts (an endonuclease, an RNA-dependent RNA polymerase and a cap-binding domain) and two structural domains (an arm domain with a blocker motif and a carboxy-terminal lariat domain). The SFTSV L protein has a compact architecture in which its cap-binding pocket is surprisingly occupied by an Arg finger of the blocker motif, and the endonuclease active centre faces back towards the cap-binding pocket, suggesting that domain rearrangements are necessary to acquire the pre-initiation state of the active site. Our results provide insight into the complete architecture of sNSRV-encoded L protein and further the understanding of sNSRV transcription initiation.
History
DepositionOct 15, 2019-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l42
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7alp
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0828.png

Downloads & links

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Map

FileDownload / File: emd_0828.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0085 / Movie #1: 0.0085
Minimum - Maximum-0.028280538 - 0.061401226
Average (Standard dev.)0.000011703104 (±0.0020826738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z237.600237.600237.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0280.0610.000

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Supplemental data

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Sample components

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Entire : Virus polymerase

EntireName: Virus polymerase
Components
  • Complex: Virus polymerase
    • Protein or peptide: RNA polymerase
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Virus polymerase

SupramoleculeName: Virus polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Phlebovirus WCH/97/HN/China/2011

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Macromolecule #1: RNA polymerase

MacromoleculeName: RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phlebovirus WCH/97/HN/China/2011
Molecular weightTheoretical: 238.813797 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCB1His (others)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMNLEV LCGRINVENG LSLGEPGLYD QIYDRPGLPD LDVTVDATGV TVDIGAVPDS ASQLGSSIN AGLITIQLSE AYKINHDFTF SGLSKTTDRR LSEVFPITHD GSDGMTPDVI HTRLDGTIVV VEFTTTRSHN I GGLEAAYR ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMNLEV LCGRINVENG LSLGEPGLYD QIYDRPGLPD LDVTVDATGV TVDIGAVPDS ASQLGSSIN AGLITIQLSE AYKINHDFTF SGLSKTTDRR LSEVFPITHD GSDGMTPDVI HTRLDGTIVV VEFTTTRSHN I GGLEAAYR TKIEKYRDPI SRRVDIMENP RVFFGVIVVS SGGVLSNMPL TQDEAEELMY RFCIANEIYT KARSMDADIE LQ KSEEELE AISRALSFFS LFEPNIERVE GTFPNSEIEM LEQFLSTPAD VDFITKTLKA KEVEAYADLC DSHYLKPEKT IQE RLEINR CEAIDKTQDL LAGLHARSNK QTSLNRGTVK LPPWLPKPSS ESIDIKTDSG FGSLMDHGAY GELWAKCLLD VSLG NVEGV VSDPAKELDI AISDDPEKDT PKEAKITYRR FKPALSSSAR QEFSLQGVEG KKWKRMAANQ KKEKESHDAL SPFLD VEDI GDFLTFNNLL ADSRYGDESV QRAVSILLEK ASAMQDTELT HALNDSFKRN LSSNVVQWSL WVSCLAQELA SALKQH CRA GEFIIKKLKF WPIYVIIKPT KSSSHIFYSL GIRKADVTRR LTGRVFSETI DAGEWELTEF KSLKTCKLTN LVNLPCT ML NSIAFWREKL GVAPWLVRKP CSELREQVGL TFLISLEDKS KTEEIITLTR YTQMEGFVSP PMLPKPQKML GKLDGPLR T KLQVYLLRKH LDCMVRIASQ PFSLIPREGR VEWGGTFHAI SGRSTNLENM VNSWYIGYYK NKEESTELNA LGEMYKKIV EMEEDKPSSP EFLGWGDTDS PKKHEFSRSF LRAACSSLER EIAQRHGRQW KQNLEERVLR EIGTKNILDL ASMKATSNFS KDWELYSEV QTKEYHRSKL LEKMATLIEK GVMWYIDAVG QAWKAVLDDG CMRICLFKKN QHGGLREIYV MDANARLVQF G VETMARCV CELSPHETVA NPRLKNSIIE NHGLKSARSL GPGSININSS NDAKKWNQGH YTTKLALVLC WFMPAKFHRF IW AAISMFR RKKMMVDLRF LAHLSSKSES RSSDPFREAM TDAFHGNREV SWMDKGRTYI KTETGMMQGI LHFTSSLLHS CVQ SFYKSY FVSKLKEGYM GESISGVVDV IEGSDDSAIM ISIRPKSDMD EVRSRFFVAN LLHSVKFLNP LFGIYSSEKS TVNT VYCVE YNSEFHFHRH LVRPTLRWIA ASHQISETEA LASRQEDYSN LLTQCLEGGA SFSLTYLIQC AQLLHHYMLL GLCLH PLFG TFMGMLISDP DPALGFFLMD NPAFAGGAGF RFNLWRACKT TDLGRKYAYY FNEIEGKTKG DEDYRALDAT SGGTLS HSV MVYWGDRKKY QALLNRMGLP EDWVEQIDEN PGVLYRRAAN KKELLLKLAE KVHSPGVTSS LSKGHVVPRV VAAGVYL LS RHCFRFSSSI HGRGSTQKAS LIKLLMMSSI SAMKHGGSLN PNQERMLFPQ AQEYDRVCTL LEEVEHLTGK FVVRERNI V RSRIDLFQEP VDLRCKAEDL VSEVWFGLKR TKLGPRLLKE EWDKLRASFA WLSTDPSETL RDGPFLSHVQ FRNFIAHVD AKSRSVRLLG APVKKSGGVT TISQVVRMNF FPGFSLEAEK SLDNQERLES ISILKHVLFM VLNGPYTEEY KLEMIIEAFS TLVIPQPSE VIRKSRTMTL CLLSNYLSSR GGSILDQIER AQSGTLGGFS KPQKTFIRPG GGVGYKGKGV WTGVMEDTHV Q ILIDGDGT SNWLEEIRLS SDARLYDVIE SIRRLCDDLG INNRVASAYR GHCMVRLSGF KIKPASRTDG CPVRIMERGF RI RELQNPD EVKMRVRGDI LNLSVTIQEG RVMNILSYRP RDTDISESAA AYLWSNRDLF SFGKKEPSCS WICLKTLDNW AWS HASVLL ANDRKTQGID NRAMGNIFRD CLEGSLRKQG LMRSKLTEMV EKNVVPLTTQ ELVDILEEDI DFSDVIAVEL SEGS LDIES IFDGAPILWS AEVEEFGEGV VAVSYSSKYY HLTLMDQAAI TMCAIMGKEG CRGLLTEKRC MAAIREQVRP FLIFL QIPE DSISWVSDQF CDSRGLDEES TIMWG

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147344
Image recording ID1

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