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- EMDB-15615: Structure of the SFTSV L protein bound in a resting state [RESTING] -
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Open data
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Basic information
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Title | Structure of the SFTSV L protein bound in a resting state [RESTING] | ||||||||||||
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Function / homology | ![]() host cell endoplasmic reticulum / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Williams HM / Thorkelsson SR / Vogel D / Milewski M / Busch C / Cusack S / Grunewald K / Quemin ERJ / Rosenthal M | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into viral genome replication by the severe fever with thrombocytopenia syndrome virus L protein. Authors: Harry M Williams / Sigurdur R Thorkelsson / Dominik Vogel / Morlin Milewski / Carola Busch / Stephen Cusack / Kay Grünewald / Emmanuelle R J Quemin / Maria Rosenthal / ![]() ![]() Abstract: Severe fever with thrombocytopenia syndrome virus (SFTSV) is a phenuivirus that has rapidly become endemic in several East Asian countries. The large (L) protein of SFTSV, which includes the RNA- ...Severe fever with thrombocytopenia syndrome virus (SFTSV) is a phenuivirus that has rapidly become endemic in several East Asian countries. The large (L) protein of SFTSV, which includes the RNA-dependent RNA polymerase (RdRp), is responsible for catalysing viral genome replication and transcription. Here, we present 5 cryo-electron microscopy (cryo-EM) structures of the L protein in several states of the genome replication process, from pre-initiation to late-stage elongation, at a resolution of up to 2.6 Å. We identify how the L protein binds the 5' viral RNA in a hook-like conformation and show how the distal 5' and 3' RNA ends form a duplex positioning the 3' RNA terminus in the RdRp active site ready for initiation. We also observe the L protein stalled in the early and late stages of elongation with the RdRp core accommodating a 10-bp product-template duplex. This duplex ultimately splits with the template binding to a designated 3' secondary binding site. The structural data and observations are complemented by in vitro biochemical and cell-based mini-replicon assays. Altogether, our data provide novel key insights into the mechanism of viral genome replication by the SFTSV L protein and will aid drug development against segmented negative-strand RNA viruses. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 71.2 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 789.8 KB | Display | ![]() |
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Full document | ![]() | 789.3 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8asgMC ![]() 8as6C ![]() 8as7C ![]() 8asbC ![]() 8asdC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15615_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15615_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Structure of the SFTSV L protein bound in a resting state [RESTING]
Entire | Name: Structure of the SFTSV L protein bound in a resting state [RESTING] |
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Components |
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-Supramolecule #1: Structure of the SFTSV L protein bound in a resting state [RESTING]
Supramolecule | Name: Structure of the SFTSV L protein bound in a resting state [RESTING] type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 238 KDa |
-Supramolecule #2: RNA-dependent RNA-polymerase L protein
Supramolecule | Name: RNA-dependent RNA-polymerase L protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: RNA
Supramolecule | Name: RNA / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: RNA-dependent RNA-polymerase L protein
Macromolecule | Name: RNA-dependent RNA-polymerase L protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 235.6985 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MNLEVLCGRI NVENGLSLGE PGLYDQIYDR PGLPDLDVTV DATGVTVDIG AVPDSASQLG SSINAGLITI QLSEAYKINH DFTFSGLSK TTDRRLSEVF PITHDGSDGM TPAVIHTRLD GTIVVVEFST TRSHNIGGLE AAYRTKIEKY RDPISRRVDI M ENPRVFFG ...String: MNLEVLCGRI NVENGLSLGE PGLYDQIYDR PGLPDLDVTV DATGVTVDIG AVPDSASQLG SSINAGLITI QLSEAYKINH DFTFSGLSK TTDRRLSEVF PITHDGSDGM TPAVIHTRLD GTIVVVEFST TRSHNIGGLE AAYRTKIEKY RDPISRRVDI M ENPRVFFG VIVVSSGGVL SNMPLTQDEA EELMYRFCIA NEIYTKARSM DADIELQKSE EELEAISRAL SFFSLFEPNI ER VEGTFPN SEIKMLEQFL STPADVDFIT KTLKAKEVEA YADLCDSHYL KPEKTIQERL EINRCEAIDK TQDLLAGLHA RSN KQTSLN RGTVKLPPWL PKPSSESIDI KTDSGFGSLM DHGAYGELWA KCLLDVSLGN VEGVVSDPAK ELDIAISDDP EKDT PKEAK ITYRRFKPAL SSSARQEFSL QGVEGKKWKR MAANQKKEKE SHETLSPFLD VEDIGDFLTF NNLLTDSRYG DESIQ RAVS ILLEKASAMQ DTELTHALND SFKRNLSSNV VQWSLWVSCL AQELASALKQ HCRAGEFIIK KLKFWPIYVI IKPTKS SSH IFYSLGIRKA DVTRRLTGRV FSDTIDAGEW ELTEFKSLKT CKLTNLVNLP CTMLNSIAFW REKLGVAPWL VRKPCSE LR EQVGLTFLIS LEDKSKTEEI ITLTRYTQME GFVSPPMLPK PQKMLGKLDG PLRTKLQVYL LRKHLDCMVR IASQPFSL I PREGRVEWGG TFHAISGRST NLENMVNSWY IGYYKNKEES TELNALGEMY KKIVEMEEDK PSSPEFLGWG DTDSPKKHE FSRSFLRAAC SSLEREIAQR HGRQWKQNLE ERVLREIGTK NILDLASMKA TSNFSKDWEL YSEVQTKEYH RSKLLEKMAT LIEKGVMWY IDAVGQAWKA VLDDGCMRIC LFKKNQHGGL REIYVMDANA RLVQFGVETM ARCVCELSPH ETVANPRLKN S IIENHGLK SARSLGPGSI NINSSNDAKK WNQGHYTTKL ALVLCWFMPA KFHRFIWAAI SMFRRKKMMV DLRFLAHLSS KS ESRSSDP FREAMTDAFH GNRDVSWMDK GRTYIKTETG MMQGILHFTS SLLHSCVQSF YKSYFVSKLK EGYMGESISG VVD VIEGSD DSAIMISIRP KSDMDEVRSR FFVANLLHSV KFLNPLFGIY SSEKSTVNTV YCVEYNSEFH FHRHLVRPTL RWIA ASHQI SETEALASRQ EDYSNLLTQC LEGGASFSLT YLIQCAQLLH HYMLLGLCLH PLFGTFMGML ISDPDPALGF FLMDN PAFA GGAGFRFNLW RACKTTDLGR KYAYYFNEIQ GKTKGDEDYR ALDATSGGTL SHSVMVYWGD RKKYQALLNR MGLPED WVE QIDENPGVLY RRAANKKELL LKLAEKVHSP GVTSSLSKGH VVPRVVAAGV YLLSRHCFRF SSSIHGRGST QKASLIK LL MMSSISAMKH GGSLNPNQER MLFPQAQEYD RVCTLLEEVE HLTGKFVVRE RNIVRSRIDL FQEPVDLRCK AEDLVSEV W FGLKRTKLGP RLLKEEWDKL RASFAWLSTD PSETLRDGPF LSHVQFRNFI AHVDAKSRSV RLLGAPVKKS GGVTTISQV VRMNFFPGFS LEAEKSLDNQ ERLESISILK HVLFMVLNGP YTEEYKLEMI IEAFSTLVIP QPSEVIRKSR TMTLCLLSNY LSSRGGSIL DQIERAQSGT LGGFSKPQKT FVRPGGGVGY KGKGVWTGVM EDTHVQILID GDGTSNWLEE IRLSSDARLY D VIESIRRL CDDLGINNRV ASAYRGHCMV RLSGFKIKPA SRTDGCPVRI MERGFRIREL QNPDEVKMRV RGDILNLSVT IQ EGRVMNI LSYRPRDTDI SESAAAYLWS NRDLFSFGKK EPSCSWICLK TLDNWAWSHA SVLLANDRKT QGIDNRAMGN IFR DCLEGS LRKQGLMRSK LTEMVEKNVV PLTTQELVDI LEEDIDFSDV IAVELSEGSL DIESIFDGAP ILWSAEVEEF GEGV VAVSY SSKYYHLTLM DQAAITMCAI MGKEGCRGLL TEKRCMAAIR EQVRPFLIFL QIPEDSISWV SDQFCDSRGL DEEST IMWG |
-Macromolecule #2: RNA (5'-R(*GP*AP*UP*CP*UP*GP*GP*GP*CP*GP*GP*UP*CP*UP*UP*UP*GP*UP*...
Macromolecule | Name: RNA (5'-R(*GP*AP*UP*CP*UP*GP*GP*GP*CP*GP*GP*UP*CP*UP*UP*UP*GP*UP*GP*U*)-3') type: rna / ID: 2 Details: The UG in the structure represents the 3/4 nts, not as it is aligned here. Number of copies: 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.410768 KDa |
Sequence | String: GAUCUGGGCG GUCUUUGUGU |
-Macromolecule #3: RNA (5'-R(*AP*CP*AP*CP*AP*GP*AP*GP*AP*CP*GP*CP*CP*CP*AP*GP*AP*UP*...
Macromolecule | Name: RNA (5'-R(*AP*CP*AP*CP*AP*GP*AP*GP*AP*CP*GP*CP*CP*CP*AP*GP*AP*UP*GP*A*)-3') type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.451975 KDa |
Sequence | String: ACACAGAGAC GCCCAGAUGA |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |