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- EMDB-31180: Structure of monomeric complex of MACV L bound to Z and 3'-vRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-31180
TitleStructure of monomeric complex of MACV L bound to Z and 3'-vRNA
Map dataMonomeric complex of MACV L bound to Z and 3'-vRNA
Sample
  • Complex: Machupo virus polymerase in complex with Z matrix protein and 3'-vRNA in monomeric form
    • Complex: Machupo virus polymerse
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: Machupo virus Z martix protein
      • Protein or peptide: RING finger protein Z
    • Complex: 3'-vRNA promoter
      • RNA: 3'-vRNA promoter
  • Ligand: MANGANESE (II) ION
  • Ligand: ZINC ION
Function / homology
Function and homology information


negative stranded viral RNA replication / cap snatching / viral budding via host ESCRT complex / 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 / cap snatching / viral budding via host ESCRT complex / 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
RING finger protein Z, zinc finger / RING finger protein Z, arenaviridae / Protein Z, RING-type zinc finger superfamily / P-11 zinc finger / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L / RING finger protein Z
Similarity search - Component
Biological speciesMachupo mammarenavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsXu X / Peng R / Peng Q / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000 China
CitationJournal: 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
DepositionApr 9, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7elc
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31180.png

Downloads & links

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Map

FileDownload / File: emd_31180.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomeric complex of MACV L bound to Z and 3'-vRNA
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.099572614 - 0.19215533
Average (Standard dev.)0.0001244974 (±0.0033799338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1000.1920.000

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Supplemental data

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Sample components

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Entire : Machupo virus polymerase in complex with Z matrix protein and 3'-...

EntireName: Machupo virus polymerase in complex with Z matrix protein and 3'-vRNA in monomeric form
Components
  • Complex: Machupo virus polymerase in complex with Z matrix protein and 3'-vRNA in monomeric form
    • Complex: Machupo virus polymerse
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: Machupo virus Z martix protein
      • Protein or peptide: RING finger protein Z
    • Complex: 3'-vRNA promoter
      • RNA: 3'-vRNA promoter
  • Ligand: MANGANESE (II) ION
  • Ligand: ZINC ION

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Supramolecule #1: Machupo virus polymerase in complex with Z matrix protein and 3'-...

SupramoleculeName: Machupo virus polymerase in complex with Z matrix protein and 3'-vRNA in monomeric form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Machupo mammarenavirus
Molecular weightExperimental: 270 KDa

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Supramolecule #2: Machupo virus polymerse

SupramoleculeName: Machupo virus polymerse / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Machupo mammarenavirus
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Machupo virus Z martix protein

SupramoleculeName: Machupo virus Z martix protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Supramolecule #4: 3'-vRNA promoter

SupramoleculeName: 3'-vRNA promoter / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Machupo mammarenavirus
Molecular weightTheoretical: 250.416062 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: 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

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Macromolecule #2: RING finger protein Z

MacromoleculeName: RING finger protein Z / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Machupo mammarenavirus
Molecular weightTheoretical: 10.660265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGNCNKPPKR PPNTQTSSNQ PSAEFRRTAP PSLYGRYNCK CCWFADTNLI TCNDHYLCLR CHQTMLRNSE LCHICWKPLP TSITVPVEP SAPPP

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Macromolecule #3: 3'-vRNA promoter

MacromoleculeName: 3'-vRNA promoter / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Machupo mammarenavirus
Molecular weightTheoretical: 6.069649 KDa
SequenceString:
GCCUAGGAUC CACUGUGCG

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Support film - Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-18 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3930000
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: EMDB MAP
EMDB ID:

0707

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 180190
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6kld

,

5i72

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7elc:
Structure of monomeric complex of MACV L bound to Z and 3'-vRNA

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