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Yorodumi- EMDB-31975: Cryo-EM structure of Machupo virus polymerase L in complex with m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31975 | |||||||||
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Title | Cryo-EM structure of Machupo virus polymerase L in complex with matrix protein Z | |||||||||
Map data | Cryo-EM structure of Machupo virus L-Z complex | |||||||||
Sample |
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Function / homology | Function and homology information RNA-templated viral transcription / negative stranded viral RNA replication / detection of maltose stimulus / maltose transport complex / viral budding via host ESCRT complex / cap snatching / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...RNA-templated viral transcription / negative stranded viral RNA replication / detection of maltose stimulus / maltose transport complex / viral budding via host ESCRT complex / cap snatching / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / viral budding from plasma membrane / virion component / outer membrane-bounded periplasmic space / host cell cytoplasm / periplasmic space / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA damage response / host cell plasma membrane / RNA binding / zinc ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Machupo mammarenavirus / Machupo virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Zhang X / Ma J / Zhang S | |||||||||
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_31975.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-31975-v30.xml emd-31975.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_31975.png | 219.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31975 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31975 | HTTPS FTP |
-Validation report
Summary document | emd_31975_validation.pdf.gz | 354 KB | Display | EMDB validaton report |
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Full document | emd_31975_full_validation.pdf.gz | 353.6 KB | Display | |
Data in XML | emd_31975_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_31975_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31975 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31975 | HTTPS FTP |
-Related structure data
Related structure data | 7vgqMC 7vh1C 7vh2C 7vh3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31975.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Machupo virus L-Z complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6 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 in complex with matrix protein Z
Entire | Name: Machupo virus polymerase in complex with matrix protein Z |
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Components |
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-Supramolecule #1: Machupo virus polymerase in complex with matrix protein Z
Supramolecule | Name: Machupo virus polymerase in complex with matrix protein Z type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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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 |
-Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,RING finger protein Z
Macromolecule | Name: Maltose/maltodextrin-binding periplasmic protein,RING finger protein Z type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Machupo virus |
Molecular weight | Theoretical: 54.913883 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHHHK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN L QEPYFTWP ...String: MHHHHHHHHK IEEGKLVIWI NGDKGYNGLA EVGKKFEKDT GIKVTVEHPD KLEEKFPQVA ATGDGPDIIF WAHDRFGGYA QSGLLAEIT PDKAFQDKLY PFTWDAVRYN GKLIAYPIAV EALSLIYNKD LLPNPPKTWE EIPALDKELK AKGKSALMFN L QEPYFTWP LIAADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLVDLI KNKHMNADTD YSIAEAAFNK GETAMTINGP WA WSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EEL AKDPRI AATMENAQKG EIMPNIPQMS AFWYAVRTAV INAASGRQTV DEALKDAQTN SSSNNNNNNN NNNLGIELEV LFQG PGSGN CNKPPKRPPN TQTSAAQPSA EFRRTALPSL YGRYNCKCCW FADTNLITCN DHYLCLRCHQ TMLRNSELCH ICWKP LPTS ITVPVEPSAP PP |
-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
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 492364 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |