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- EMDB-31975: Cryo-EM structure of Machupo virus polymerase L in complex with m... -

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Basic information

Entry
Database: EMDB / ID: EMD-31975
TitleCryo-EM structure of Machupo virus polymerase L in complex with matrix protein Z
Map dataCryo-EM structure of Machupo virus L-Z complex
Sample
  • Complex: Machupo virus polymerase in complex with matrix protein Z
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RING finger protein Z
  • Ligand: ZINC ION
KeywordsPolymerase / matrix protein / complex / VIRAL PROTEIN
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / detection of maltose stimulus / cap snatching / viral budding via host ESCRT complex / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...RNA-templated viral transcription / negative stranded viral RNA replication / detection of maltose stimulus / cap snatching / viral budding via host ESCRT complex / maltose transport complex / 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 / viral budding from plasma membrane / cell chemotaxis / virion component / outer membrane-bounded periplasmic space / Hydrolases; Acting on ester bonds / host cell cytoplasm / periplasmic space / hydrolase activity / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA damage response / host cell plasma membrane / RNA binding / zinc ion binding / metal ion binding / membrane
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 ...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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / RNA-directed RNA polymerase L / RING finger protein Z
Similarity search - Component
Biological speciesMachupo mammarenavirus / Machupo virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZhang X / Ma J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionSep 18, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7vgq
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31975.png

Downloads & links

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Map

FileDownload / File: emd_31975.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Machupo virus L-Z complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 120 pix.
= 192. Å		1.6 Å/pix.
x 120 pix.
= 192. Å		1.6 Å/pix.
x 120 pix.
= 192. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067 / Movie #1: 0.067
Minimum - Maximum-0.3748704 - 0.5411106
Average (Standard dev.)0.0010858312 (±0.016655369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 192.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.61.61.6
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z192.000192.000192.000
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.3750.5410.001

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Supplemental data

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Sample components

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Entire : Machupo virus polymerase in complex with matrix protein Z

EntireName: Machupo virus polymerase in complex with matrix protein Z
Components
  • Complex: Machupo virus polymerase in complex with matrix protein Z
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RING finger protein Z
  • Ligand: ZINC ION

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Supramolecule #1: Machupo virus polymerase in complex with matrix protein Z

SupramoleculeName: Machupo virus polymerase in complex with matrix protein Z
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Machupo mammarenavirus

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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 virus
Molecular weightTheoretical: 253.456344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,RING finger protein Z

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,RING finger protein Z
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Machupo virus
Molecular weightTheoretical: 54.913883 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, RING finger protein Z

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

0707

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 492364
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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