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Yorodumi- EMDB-30388: Structure of Machupo virus polymerase bound to Z matrix protein (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30388 | |||||||||
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Title | Structure of Machupo virus polymerase bound to Z matrix protein (monomeric complex) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information negative stranded viral RNA replication / viral budding via host ESCRT complex / cap snatching / viral budding from plasma membrane / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / RNA-directed RNA polymerase ...negative stranded viral RNA replication / viral budding via host ESCRT complex / cap snatching / viral budding from plasma membrane / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / 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: 3.37 Å | |||||||||
Authors | Xu X / Peng R / Peng Q / Shi Y | |||||||||
Citation | Journal: Nat Microbiol / Year: 2021 Title: Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals. Authors: Xin Xu / Ruchao Peng / Qi Peng / Min Wang / Ying Xu / Sheng Liu / Xiaolin Tian / Haiteng Deng / Yimin Tong / Xiaoyou Hu / Jin Zhong / Peiyi Wang / Jianxun Qi / George F Gao / Yi Shi / Abstract: Zoonotic arenaviruses can lead to life-threating diseases in humans. These viruses encode a large (L) polymerase that transcribes and replicates the viral genome. At the late stage of replication, ...Zoonotic arenaviruses can lead to life-threating diseases in humans. These viruses encode a large (L) polymerase that transcribes and replicates the viral genome. At the late stage of replication, the multifunctional Z protein interacts with the L polymerase to shut down RNA synthesis and initiate virion assembly. However, the mechanism by which the Z protein regulates the activity of L polymerase is unclear. Here, we used cryo-electron microscopy to resolve the structures of both Lassa and Machupo virus L polymerases in complex with their cognate Z proteins, and viral RNA, to 3.1-3.9 Å resolutions. These structures reveal that Z protein binding induces conformational changes in two catalytic motifs of the L polymerase, and restrains their conformational dynamics to inhibit RNA synthesis, which is supported by hydrogen-deuterium exchange mass spectrometry analysis. Importantly, we show, by in vitro polymerase reactions, that Z proteins of Lassa and Machupo viruses can cross-inhibit their L polymerases, albeit with decreased inhibition efficiencies. This cross-reactivity results from a highly conserved determinant motif at the contacting interface, but is affected by other variable auxiliary motifs due to the divergent evolution of Old World and New World arenaviruses. These findings could provide promising targets for developing broad-spectrum 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_30388.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-30388-v30.xml emd-30388.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30388_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_30388.png | 189 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30388 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30388 | HTTPS FTP |
-Validation report
Summary document | emd_30388_validation.pdf.gz | 365.9 KB | Display | EMDB validaton report |
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Full document | emd_30388_full_validation.pdf.gz | 365.5 KB | Display | |
Data in XML | emd_30388_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_30388_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30388 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30388 | HTTPS FTP |
-Related structure data
Related structure data | 7ckmMC 7cklC 7el9C 7elaC 7elbC 7elcC 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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-Map
File | Download / File: emd_30388.map.gz / Format: CCP4 / Size: 52.7 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: 1.08 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 Z matrix protein
Entire | Name: Machupo virus polymerase in complex with Z matrix protein |
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Components |
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-Supramolecule #1: Machupo virus polymerase in complex with Z matrix protein
Supramolecule | Name: Machupo virus polymerase in complex with Z matrix protein type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Machupo mammarenavirus |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Experimental: 260 KDa |
-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: 250.416062 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDEYVQELKG LIRKHIPERC EFGHQKVTFL SQVHPSPLLT EGFKLLSSLV ELESCEAHAC QANTDQRFVD VILSDNGILC PTLPKVIPD GFKLTGKTLI LLETFVRVNP DEFEKKWKAD MSKLLNLKHD LQKSGVTLVP IVDGRSNYNN RFVADWVIER I RWLLIEIL ...String: MDEYVQELKG LIRKHIPERC EFGHQKVTFL SQVHPSPLLT EGFKLLSSLV ELESCEAHAC QANTDQRFVD VILSDNGILC PTLPKVIPD GFKLTGKTLI LLETFVRVNP DEFEKKWKAD MSKLLNLKHD LQKSGVTLVP IVDGRSNYNN RFVADWVIER I RWLLIEIL KASKSMLEID IEDQEYQRLI HSLSNVKNQS LGLENLEHLK RNSLDYDERL NESLFIGLKG DIRESTVREE LI KLKLWFK DEVFSKGLGK FKLTDRRELL ESLSSLGAHL DSDVSSCPFC NNKLMEIVYN VTFSCVERTD GVATVDQQFS TTH SNIEKH YLSVLSLCNK IKGLKVFNTR RNTLLFLDLI MVNLMVDISD SCQDAIESLR KSGLIVGQMV MLVNDRVLDI LEAV KLIRK KIGTNPNWVK NCSKILERSH PEIWHHLSTL IKQPDFNSLI SIAQHLVSDR PIMRYSVERG SDKICRHKLF QEMSS FEQM RLFKTLSSIS LSLINSMKTS FSSRLLVNER EFSKYFGNVR LRECYAQRFY LAESLVGFLF YQKTGERSRC YSVYLS DNG VMSEQGSFYC DPKRFFLPVF SDEVLAGMCE EMTSWLDFDT GLMNDTGPIL RLLVLAILCS PSKRNQTFLQ GLRYFLM AF ANQIHHIDLT SKLVVECKSS SEVVVQRLAV GLFIRLLSGE SDASLFFSRR FKYLLNVSYL CHLITKETPD RLTDQIKC F EKFIEPKVKF GCAVVNPSLN GKLTVDQEDI MINGLKKFFS KSLRDTEDVQ TPGVCKELLN YCVSLFNRGK LKVSGELKN NPFRPNITST ALDLSSNKSV VIPKLDELGN ILSTYDKEKL VSACVSSMAE RFKTKGRYNL DPDSTDYLIL KNLTGLVSAG PKAKSTQEE LSLMYEALTE EQVESFNEIK HDVQVALAKM ADNSVNTRTK NLGRADNSVK NGNNPLDNLW SPFGVMKEIR A EVSLHEVK DFDPDVLPPE VYKELCDAVY KSSEKCNFFL EGVLDVCPLG LLLKNLTTSS YVDEEYFMCF 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 LNGQI PSHI MSVLDMGQGI LHNTSDLYGL ITEQFLCYAL DLLYDVIPVS YTSSDDQITL IKTPSLDIEG GSDAAEWLEM ICFHEF LSS KLNKFVSPKS VIGTFVAEFK SRFFVMGEET PLLTKFVAAA LHNVKCKTPT QLSETIDTIC DQCIANGVST KIVTRIS KR VNQLIRYSGY GETPFGAIED QDVKDWVDGS RGYRLQRKIE AIFHDDKETS FIRNCARKVF NDIKRGRIFE ENLINLIG R GGDEALTGFL QYAGCSEQEV NRVLNYRWVN LSSFGDLRLV LRTKLMTSRR VLEREEVPTL IKTLQSKLSR NFTKGVKKI LAESINKSAF QSSVASGFIG FCKSMGSKCV RDGKGGFLYI KEVYSGVSAC TCEICALKPK IIYCNNSLNK VSQFSKPILW DYFSLVLTN ACELGEWVFS TVKEPQKPLV LNNQNFFWAV KPKVVRQIED QLGMNHVLQS IRRNYPVLFD EHLTPFMNDL Q VSRTMDSG RLKFLDVCIA LDMMNENLGI ISHLLKTRDN SVYIVKQSDC ALAHIRQSSY TDWELGLSPQ QICTNFKTQL VL SSMVNPL VLSTSCLKSF FWFNEVLELE DDSQIELAEL TDFALMVKNQ NVSRAMFVED IAMGYVVSNF EGVRISLSNV MVD GVQLPP QEKAPDIGEL FGLKAENVIV GLVVQIDHVR MSTKFKLKRK MVYSFSLECI MDVGEIQNKE VILKVVAVDQ SVSG SGGNH MLLDGVSVVA SLPLFTGQAS FDLAAMLIES NLAGSNDNFL MRNVTLDLGG FSPELSDKYS YRLSGPENQE DPLVL KDGA FYVGGERLST YKVEFTGDLV VKALGALEDD ESVVSMLHQL WPYLKATSQV ILFQQEDFTI VHDLYKKQLT KSIESF GEW IEFTNFKVAY SKSLKELVIS DTQGSFRLKG VMCRPLASTP QVEDIE |
-Macromolecule #2: RING finger protein Z
Macromolecule | Name: 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: 10.660265 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGNCNKPPKR PPNTQTSSNQ PSAEFRRTAP PSLYGRYNCK CCWFADTNLI TCNDHYLCLR CHQTMLRNSE LCHICWKPLP TSITVPVEP SAPPP |
-Macromolecule #3: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / 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 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
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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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-17 / 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 / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |