+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31985 | |||||||||
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Title | Cryo-EM structure of Machupo virus polymerase L | |||||||||
Map data | Cryo-EM structure of Machupo virus polymerase L | |||||||||
Sample |
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Function / homology | Function and homology information RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Machupo mammarenavirus / Machupo virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Ma J / Zhang S / Zhang X | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of Machupo virus polymerase in complex with matrix protein Z. Authors: Jun Ma / Shuangyue Zhang / Xinzheng Zhang / Abstract: The Arenaviridae family includes several viruses that cause severe human hemorrhagic fevers with high mortality, with no effective countermeasures currently available. The arenavirus multi-domain L ...The Arenaviridae family includes several viruses that cause severe human hemorrhagic fevers with high mortality, with no effective countermeasures currently available. The arenavirus multi-domain L protein is involved in viral transcription and replication and represents a promising target for antiviral drugs. The arenavirus matrix protein Z is a small multi-functional protein that inhibits the activities of the L protein. Here we report the structure of Machupo virus L protein in complex with Z determined by cryo-electron microscopy. The Z protein acts as a staple and binds the L protein with 1:1 stoichiometry at the intersection between the PA-C-like region, RNA-dependent RNA polymerase and PB2-N-like region. Binding of the Z protein may lock the multiple domains of L into a fixed arrangement leading to loss of catalytic activity. These results further our understanding of the inhibitory mechanism of arenavirus replication machinery and provide a novel perspective to develop antiviral drugs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31985.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-31985-v30.xml emd-31985.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_31985.png | 168.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31985 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31985 | HTTPS FTP |
-Related structure data
Related structure data | 7vh3MC 7vgqC 7vh1C 7vh2C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31985.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Machupo virus polymerase L | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Machupo virus Polymerase L
Entire | Name: Machupo virus Polymerase L |
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Components |
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-Supramolecule #1: Machupo virus Polymerase L
Supramolecule | Name: Machupo virus Polymerase L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Machupo mammarenavirus |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-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: Machupo virus |
Molecular weight | Theoretical: 253.456344 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDEYVQELKG LIRKHIPDRC EFAHQKVTFL SQVHPSPLLT EGFKLLSSLV ELESCEAHAC QANTDQRFVD VILSDNGILC PTLPKVIPD GFKLTGKTLI LLETFVRVNP DEFEKKWKAD MSKLLNLKHD LQKSGVTLVP IVDGRSNYNN RFVADWVIER M RWLLIEIL ...String: MDEYVQELKG LIRKHIPDRC EFAHQKVTFL SQVHPSPLLT EGFKLLSSLV ELESCEAHAC QANTDQRFVD VILSDNGILC PTLPKVIPD GFKLTGKTLI LLETFVRVNP DEFEKKWKAD MSKLLNLKHD LQKSGVTLVP IVDGRSNYNN RFVADWVIER M RWLLIEIL KASKSMLEID IEDQEYQRLI HSLSNVKNQS LGLENLEHLK RNSLDYDERL NESLFIGLKG DIRESTVREE LI KLKMWFK DEVFSKGLGK FKLTDRRELL ESLSSLGAHL DSDVSSCPFC NNKLMEIVYN VTFSSVERTD GAATVDQQFS TTH TNIEKH YLSVLSLCNK IKGLKVFNTR RNTLLFLDLI MVNLMVDISE SCQDAIESLR KSGLIVGQMV MLVNDRVLDI LEAI KLIRK KIGTNPNWVK NCSKILERSH PEIWLQLNTL IRQPDFNSLI SIAQYLVSDR PIMRYSVERG SDKICRHKLF QEMSS FEQM RLFKTLSSIS LSLINSMKTS FSSRLLVNER EFSKYFGNVR LRECYAQRFY LAESLVGFLF YQKTGERSRC YSVYLS DNG VMSEQGSFYC DPKRFFLPVF SDEVLAGMCE EMTSWLDFDT GLMNDTGPIL RLLVLAILCS PSKRNQTFLQ GLRYFLM AF ANQIHHIDLI SKLVVECKSS SEVVVQRLAV GLFIRLLGGE SDASSFFSRR FKYLLNVSYL CHLITKETPD RLTDQIKC F EKFIEPKVKF GCAVVNPSLN GKLTVDQEDI MINGLKKFFS KSLRDTEDVQ TPGVCKELLN YCVSLFNRGK LKVSGELKN NPFRPNITST ALDLSSNKSV VIPKLDELGN ILSTYDKEKL VSACVSSMAE RFKTKGRYNL DPESTDYLIL KNLTGLVSAG PKAKSSQEE LSLMYETLTE EQVESFNEIK YDVQVALAKM ADNSVNTRIK NLGRADNSVK NGNNPLDNLW SPFGVMKEIR A EVSLHEVK DFDPDVLPSD VYKELCDAVY KSSEKCNFFL EEVLDVCPLG LLLKNLTTSS YMEEEYFMCF KYLLIQGHFD QK LGSYEHK SRSRLGFTDE TLRLKDEVRL SIRESNSEAI ADKLDKSYFT NAALRNLCFY SEDSPTEFTS ISSNSGNLKF GLS YKEQVG SNRELYVGDL NTKLMTRLVE DFSEAVGNSM KYTCLNSEKE FERAICDMKM AVNNGDLSCS YDHSKWGPTM SPAL FLALL QMLELRTPVD RSKIDLDSVK SILKWHLHKV VEVPINVAEA YCIGKLKRSL GLMGCGSTSL SEEFFHQTMQ LSGQI PSHI MSVLDMGQGI LHNTSDLYGL ITEQFLCYAL DLLYDVIPVS YTSSDDQITL VKTPSLDIEG GSDAAEWLEM ICFHEF LSS KLNKFVSPKS VIGTFVAEFK SRFFVMGEET PLLTKFVSAA LHNVKCKTPT QLSETIDTIC DQCIANGVST KIVARIS KR VNQLIRYSGY GDTPFGAIED QDVKDWVDGS RGYRLQRKIE AIFYDDKETS FIRNCARKVF NDIKRGRIFE ENLINLIG R GGDEALTGFL QYAGCSEQEV NRVLNYRWVN LSSFGDLRLV LRTKLMTSRR VLEREEVPTL IKTLQSKLSR NFTKGVKKI LAESINKSAF QSSVASGFIG FCKSMGSKCV RDGKGGFLYI KEVYSGINVC ICEICALKPK IIYCNDSLNK VSQFSKPILW DYFSLVLTN ACELGEWVFS TVKEPQKPLV LNNQNFFWAV KPKVVRQIED QLGMNHVLQS IRRNYPVLFD EHLAPFMNDL Q VSRTMDSG RLKFLDVCIA LDMMNENLGI ISHLLKTRDN SVYIVKQSDC ALAHIRQSSY TDWELGLSPQ QICTNFKTQL VL SSMVNPL VLSTSCLKSF FWFNEVLELE DDSQIELAEL TDFALMVKNQ NVSRAMFVED IAMGYVVSNF EGVRISLSNV MVD GVQLPP KEKAPDVGVL FGLKAENVIV GLVVQIDHVR MSTKFKLRRK MVYSFSLECT MDVGDIQNKE VILKVVAVDQ SVSG SGGNH MLLDGVPVIA SLPLFTGQAS FDLAAMLIES NLAGSNDNFL MSNVTLDLGG FSPELSDKYS YRLSGPENQE DPLVL KDGA FYVGGERLST YKVELTGDLV VKALGALEDD EGVVSMLHQL WPYLKATSQV ILFQQEDFTI VHDLYKIQLT KSIESF GEW IEFTNFKVAY SKSLKELVIS DTQGSFRLKG VMCRPLANTL QVEDIEWSHP QFEKGGGSGG GSGGSSAWSH PQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 332322 |