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Yorodumi- EMDB-37964: Structure of the Mumps Virus L Protein (state2) Bound by Phosphop... -
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-Basic information
Entry | Database: EMDB / ID: EMD-37964 | |||||||||
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Title | Structure of the Mumps Virus L Protein (state2) Bound by Phosphoprotein Tetramer (composite map) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mumps virus polymerase complex / RNA-dependent RNA synthesis / Large protein / phosphoprotein. / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mumps orthorubulavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 Å | |||||||||
Authors | Li TH / Shen QT | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structures of the mumps virus polymerase complex via cryo-electron microscopy. Authors: Tianhao Li / Mingdong Liu / Zhanxi Gu / Xin Su / Yunhui Liu / Jinzhong Lin / Yu Zhang / Qing-Tao Shen / Abstract: The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), ...The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L-P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has the appendage averaged out, which is inaccessible to MTase. In both conformations, parallel P tetramers are revealed around MuV L, which, together with structures of other nsNSVs, demonstrates the diverse origins of the L-binding X domain of P. Our study links varying structures of nsNSV polymerase complexes with genome replication and transcription and points to a sliding model for polymerase complexes to advance along the RNA templates. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37964.map.gz | 219.7 MB | EMDB map data format | |
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Header (meta data) | emd-37964-v30.xml emd-37964.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_37964.png | 50.9 KB | ||
Filedesc metadata | emd-37964.cif.gz | 7.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37964 | HTTPS FTP |
-Related structure data
Related structure data | 8x01MC 8izlC 8yxlC 8yxmC 8yxoC 8yxpC 8yxrC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37964.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.53 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : The MuV polymerase complex of RNA-directed RNA polymerase L with ...
Entire | Name: The MuV polymerase complex of RNA-directed RNA polymerase L with tetrameric phosphoproteins |
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Components |
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-Supramolecule #1: The MuV polymerase complex of RNA-directed RNA polymerase L with ...
Supramolecule | Name: The MuV polymerase complex of RNA-directed RNA polymerase L with tetrameric phosphoproteins type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1 Details: The MuV polymerase complex expressed in Sf9 cells and purified by affinity chromatography and size-exlusive chromatography sequentially. |
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Source (natural) | Organism: Mumps orthorubulavirus / Strain: Jeryl-Lynn |
-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: Mumps orthorubulavirus |
Molecular weight | Theoretical: 256.833094 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAGLNEILLP EVHLNSPIVR YKLFYYILHG QLPNDLEPDD LGPLANQNWK AIRAEESQVH ARLKQIRVEL IARIPSLRWT RSQREIAIL IWPRILPILQ AYDLRQSMQL PTVWEKLTQS TVNLISDGLE RVVLHISNQL TGKPNLFTRS RAGQDTKDYS I PSTRELSQ ...String: MAGLNEILLP EVHLNSPIVR YKLFYYILHG QLPNDLEPDD LGPLANQNWK AIRAEESQVH ARLKQIRVEL IARIPSLRWT RSQREIAIL IWPRILPILQ AYDLRQSMQL PTVWEKLTQS TVNLISDGLE RVVLHISNQL TGKPNLFTRS RAGQDTKDYS I PSTRELSQ IWFNNEWSGS VKTWLMIKYR MRQLITNQKT GELTDLVTIV DTRSTLCIIT PELVALYSSE HKALTYLTFE MV LMVTDML EGRLNVSSLC TASHYLSPLK KRIEVLLTLV DDLALLMGDK VYGIVSSLES FVYAQLQYGD PVIDIKGTFY GFI CNEILD LLTEDNIFTE EEANKVLLDL TSQFDNLSPD LTAELLCIMR LWGHPTLTAS QAASKVRESM CAPKVLDFQT IMKT LAFFH AILINGYRRS HNGIWPPTTL HGNAPKSLIE MRHDNSELKY EYVLKNWKSI SMLRIHKCFD ASPDEDLSIF MKDKA ISCP RQDWMGVFRR SLIKQRYRDA NRPLPQPFNR RLLLNFLEDD RFDPIKELEY VTSGEYLRDP EFCASYSLKE KEIKAT GRI FAKMTKRMRS CQVIAESLLA NHAGKLMREN GVVLDQLKLT KSLLTMNQIG IISEHSRRST ADNMTLAHSG SNKHRIN NS QFKKNKDNKH EMPDDGFEIA ACFLTTDLTK YCLNWRYQVI IPFARTLNSM YGIPHLFEWI HLRLMRSTLY VGDPFNPP S DPTQLDLDTA LNDDIFIVSP RGGIEGLCQK LWTMISISTI ILSATEANTR VMSMVQGDNQ AIAITTRVVR SLSHSEKKE QAYKASKLFF ERLRANNHGI GHHLKEQETI LSSDFFIYSK RVFYKGRILT QALKNVSKMC LTADILGDCS QASCSNLATT VMRLTENGV EKDLCYFLNA FMTIRQLCYD LVFPQTKSLS QDITNAYLNH PILISRLCLL PSQLGGLNFL SCSRLFNRNI G DPLVSAIA DVKRLIKAGC LDIWVLYNIL GRRPGKGKWS TLAADPYTLN IDYLVPSTTF LKKHAQYTLM ERSVNPMLRG VF SENAAEE EEELAQYLLD REVVMPRVAH VILAQSSCGR RKQIQGYLDS TRTIIRYSLE VRPLSAKKLN TVIEYNLLYL SYN LEIIEK PNIVQPFLNA INVDTCSIDI ARSLRKLSWA TLLNGRPIEG LETPDPIELV HGCLIIGSDE CEHCSSGDDK FTWF FLPKG IRLDDDPASN PPIRVPYIGS KTDERRVASM AYIKGASVSL KSALRLAGVY IWAFGDTEES WQDAYELAST RVNLT LEQL QSLTPLPTSA NLVHRLDDGT TQLKFTPASS YAFSSFVHIS NDCQILEIDD QVTDSNLIYQ QVMITGLALI ETWNNP PIN FSVYETTLHL HTGSSCCIRP VESCVVNPPL LPVPLINVPQ MNKFVYDPEP LSLLEMEKIE DIAYQTRIGG LDQIPLL EK IPLLAHLTAK QMVNSITGLD EATSIMNDAV VQADYTSNWI SECCYTYIDS VFVYSGWALL LELSYQMYYL RIQGIQGI L DYVYMTLRRI PGMAITGISS TISHPRILRR CINLDVIAPI NSPHIASLDY TKLSIDAVMW GTKQVLTNIS QGIDYEIVV PSESQLTLSD RVLNLVARKL SLLAIIWANY NYPPKVKGMS PEDKCQALTT HLLQTVEYVE YIQIEKTNIR RMIIEPKLTA YPSNLFYLS RKLLNAIRDS EEGQFLIASY YNSFGYLEPI LMESKIFNLS SSESASLTEF DFILNLELSD ASLEKYSLPS L LMTAENMD NPFPQPPLHH VLRPLGLSST SWYKTISVLN YISHMKISDG AHLYLAEGSG ASMSLIETFL PGETIWYNSL FN SGENPPQ RNFAPLPTQF IESVPYRLIQ AGIAAGNGIV QSFYPLWNGN SDITDLSTKT SVEYIIHKVG ADTCALVHVD LEG VPGSMN SMLERAQVHA LLITVTVLKP GGLLILKASW EPFNRFSFLL TVLWQFFSTI RILRSSYSDP NNHEVYIIAT LAVD PTTSS FTTALNRART LNEQGFSLIP PELVSEYWRK RVEQGQIIQD CIDKVISECV RDQYLADNNI ILQAGGTPST RKWLD LPDY SSFNELQSEM ARLITIHLKE VIEILKGQAS DHDTLLFTSY NVGPLGKINT ILRLIVERIL MYTVRNWCIL PTQTRL TLR QSIELGEFRL RDVITPMEIL KLSPNRKYLK SALNQSTFNH LMGETSDILL NRAYQKRIWK AIGCVIYCFG LLTPDVE GS ERIDVDNDIP DYDIHGDII UniProtKB: RNA-directed RNA polymerase L |
-Macromolecule #2: Phosphoprotein
Macromolecule | Name: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mumps orthorubulavirus / Strain: Jeryl-Lynn |
Molecular weight | Theoretical: 41.651066 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDQFIKQDET GDLIETGMNV ANHFLSTPIQ GTNSLSKASI LPGVAPVLIG NPEQKNIQHP TASHQGSKTK GRGSGVRSII VSPSEAGNG GTQIPEPLFA QTGQGGIVTT VYQDPTIQPT GSYRSVELAK IGKERMINRF VEKPRTSTPV TEFKRGGPGA A AQGQTIQE ...String: MDQFIKQDET GDLIETGMNV ANHFLSTPIQ GTNSLSKASI LPGVAPVLIG NPEQKNIQHP TASHQGSKTK GRGSGVRSII VSPSEAGNG GTQIPEPLFA QTGQGGIVTT VYQDPTIQPT GSYRSVELAK IGKERMINRF VEKPRTSTPV TEFKRGGPGA A AQGQTIQE EGIDGNGASA GSKERSGSLS GATLYAHLSL PQQDSTPANV GIAPQSAISA NEIMDLLRGM DARLQHLEQK VD KVLAQGS MVTQIKNELS TVKTTLATIE GMMATVKIMD PGNPTGVPVD ELRRSFSDHV TIVSGPGDVS FSSSEKPTLY LDE LARPVS KPRPAKQTKS QPVKDLAGQK VMITKMITDC VANPQMKQAF EQRLAKASTE DALNDIKRDI IRSAI UniProtKB: Phosphoprotein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.75 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477568 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |