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Yorodumi- EMDB-37253: Structure of Tomato spotted wilt virus L protein contained endoH ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37253 | |||||||||
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Title | Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'vRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Tomato 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-dependent RNA polymerase activity / DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Tomato spotted wilt virus (strain Bulgarian L3) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Cao L / Wang X | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Structure of Tomato spotted wilt virus L protein Authors: Cao L / Wang X | |||||||||
History |
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-Structure visualization
-Downloads & links
-EMDB archive
Map data | emd_37253.map.gz | 38.3 MB | EMDB map data format | |
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Header (meta data) | emd-37253-v30.xml emd-37253.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_37253.png | 105.5 KB | ||
Filedesc metadata | emd-37253.cif.gz | 6.7 KB | ||
Others | emd_37253_half_map_1.map.gz emd_37253_half_map_2.map.gz | 37.8 MB 37.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37253 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37253 | HTTPS FTP |
-Validation report
Summary document | emd_37253_validation.pdf.gz | 902.1 KB | Display | EMDB validaton report |
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Full document | emd_37253_full_validation.pdf.gz | 901.6 KB | Display | |
Data in XML | emd_37253_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_37253_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37253 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37253 | HTTPS FTP |
-Related structure data
Related structure data | 8ki7MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37253.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Structure of Tomato spotted wilt virus L protein contained endoH ...
Entire | Name: Structure of Tomato spotted wilt virus L protein contained endoH domain binding to 3'5'vRNA |
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Components |
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-Supramolecule #1: Structure of Tomato spotted wilt virus L protein contained endoH ...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Tomato spotted wilt virus (strain Bulgarian L3) |
-Macromolecule #1: RNA-directed RNA polymerase L
Macromolecule | Name: RNA-directed RNA polymerase L / 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: Tomato spotted wilt virus (strain Bulgarian L3) / Strain: Bulgarian L3 |
Molecular weight | Theoretical: 240.378375 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3')
Macromolecule | Name: RNA (5'-R(P*AP*GP*AP*GP*CP*AP*AP*UP*CP*A)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.208012 KDa |
Sequence | String: AGAGCAAUCA |
-Macromolecule #3: RNA (5'-R(P*GP*CP*AP*AP*UP*CP*AP*GP*G)-3')
Macromolecule | Name: RNA (5'-R(P*GP*CP*AP*AP*UP*CP*AP*GP*G)-3') / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 2.894807 KDa |
Sequence | String: GCAAUCAGG |
-Macromolecule #4: RNA (5'-R(P*AP*CP*CP*UP*GP*AP*UP*UP*GP*CP*UP*CP*U)-3')
Macromolecule | Name: 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 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.055421 KDa |
Sequence | String: ACCUGAUUGC UCU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156980 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |