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- EMDB-31163: Junin virus(JUNV) RNA polymerase L complexed with Z protein -

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Basic information

Entry
Database: EMDB / ID: EMD-31163
TitleJunin virus(JUNV) RNA polymerase L complexed with Z protein
Map datacryo-EM map for Junin virus L and Z protein complex
Sample
  • Complex: Complex of L and Z proteins of Junin virus (JUNV)
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: RING finger protein Z
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


virion component => GO:0044423 / negative stranded viral RNA replication / viral budding via host ESCRT complex / cap snatching / viral budding from plasma membrane / host cell cytoplasm / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / RNA-directed RNA polymerase ...virion component => GO:0044423 / negative stranded viral RNA replication / viral budding via host ESCRT complex / cap snatching / viral budding from plasma membrane / 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
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 speciesJunin mammarenavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen Y
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for recognition and regulation of arenavirus polymerase L by Z protein.
Authors: Huiling Kang / Jingyuan Cong / Chenlong Wang / Wenxin Ji / Yuhui Xin / Ying Qian / Xuemei Li / Yutao Chen / Zihe Rao /
Abstract: Junin virus (JUNV) causes Argentine hemorrhagic fever, a debilitating human disease of high mortality rates and a great risk to public health worldwide. Studying the L protein that replicates and ...Junin virus (JUNV) causes Argentine hemorrhagic fever, a debilitating human disease of high mortality rates and a great risk to public health worldwide. Studying the L protein that replicates and transcribes the genome of JUNV, and its regulator Z protein should provide critical clues to identify therapeutic targets for disrupting the life cycle of JUNV. Here we report the 3.54 Å cryo-EM structure of the JUNV L protein complexed with regulator Z protein. JUNV L structure reveals a conserved architecture containing signature motifs found in other L proteins. Structural analysis shows that L protein is regulated by binding of Z protein at the RNA product exit site. Based on these findings, we propose a model for the role of Z protein as a switch to turn on/off the viral RNA synthesis via its interaction with L protein. Our work unveils the mechanism of JUNV transcription, replication and regulation, which provides a framework for the rational design of antivirals for combating viral infections.
History
DepositionApr 2, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing 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-7eju
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31163.png

Downloads & links

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Map

FileDownload / File: emd_31163.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map for Junin virus L and Z protein complex
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.0123 / Movie #1: 0.01
Minimum - Maximum-0.04761791 - 0.06704811
Average (Standard dev.)-1.4322368e-05 (±0.0029717598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 166.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z166.400166.400166.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0480.067-0.000

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Supplemental data

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Sample components

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Entire : Complex of L and Z proteins of Junin virus (JUNV)

EntireName: Complex of L and Z proteins of Junin virus (JUNV)
Components
  • Complex: Complex of L and Z proteins of Junin virus (JUNV)
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: RING finger protein Z
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of L and Z proteins of Junin virus (JUNV)

SupramoleculeName: Complex of L and Z proteins of Junin virus (JUNV) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: The RNA polymerase L protein complexed with a zinc-binding Z protein
Source (natural)Organism: Junin mammarenavirus
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
Molecular weightTheoretical: 250 KDa

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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: Junin mammarenavirus
Molecular weightTheoretical: 253.499484 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MEESVNEIKT LIRKHFPERQ ELAYQRDIFL SQHHPSSLLL EGFKLLSSLV ELESCEAHAC QINSDQKFVD VILSDHGILC PTLPKVIPD GFKLTGKTLI LLETFVRVNP DEFERKWKSD MSKLLNLKSD LLRVGITLVP VVDGRSSYSN RFLADWVVER V RWLLIDIL ...String:
MEESVNEIKT LIRKHFPERQ ELAYQRDIFL SQHHPSSLLL EGFKLLSSLV ELESCEAHAC QINSDQKFVD VILSDHGILC PTLPKVIPD GFKLTGKTLI LLETFVRVNP DEFERKWKSD MSKLLNLKSD LLRVGITLVP VVDGRSSYSN RFLADWVVER V RWLLIDIL KKSKFMQEIN IEEQEYQRLI HSLSNTKNQS LGLENIECLK KNSLGYDERL NESLFVGVRG DIRESVIREE LI KLRFWFK KEIFDKQLGK FKFSQKSNLI NDLILLGSHK DSDVPSCPFC ANKLMDVVYS IALHPIDEVN MERQSDENST SID AVERCY LQALSVCNKV KGLKVFNTRR NTLLFLDLVL LNLLCDLFKT YDGAIVRLRN AGIVVGQMLM LVNDRLLDIL EAIK LIRKK LMTSPKWVQM CSRTLKNSHQ DLWLQLEKLI KHPDMDNLMI LAQVLVSDRP VMRYTIDREF EKICRHQPFS SLVEG EQKK LFRILSSISL ALVNSMKTSF SSRLLINERE YSRYFGNVRL RECYVQRFHL TKNTFGLLFY QKTGEKSRCY SIYLST NGV LEEQGSFYCD PKRFFLPIFS EDVLIEMCEE MTSWLDFSHE LMTMTRPILR LLVLAVLCSP SKRNQTFLQG LRYFLMA YA NQIHHVDLMS KLRVDCMSGS EVLIQRMAVE LFQIILSEGE DADLYFARRF KYLLNVSYLC HLVTKETPDR LTDQIKCF E KFVEPKVKFG CVVVNPPLNG SLTLEQEDTM IRGLDRFFSK EAKTSSDTQI PGVCKEILSF CISLFNRGRL KVTGELKSN PYRPNITSTA LDLSSNKSVV IPKLDELGNI LSVYDKEKLV STCVSTMAER FKTKGRYNLD PDSMDYLILK NLTGLVSTGS RTRTNQEEL SVMYESLTED QVRAFEGIRN DVQMTLAKMA NSEGSKVETS KLKSKNLSVD ERESLELLWA PFGVMREIKA E VSMHEVKD FDPDVFRSDV YKELCDTVYL SPYKLTYFLE APQDICPLGL LLKNLTTIAY QEEEFFECFK YLLIQGHYDQ KL GSYEHRS RSRLGFSSEV LKLKDEVRLS TRESNSEAIA DKLDKSYFTN AALRNLCFYS DDSPTEFTSI SSNTGNLKFG LSY KEQVGS NRELYVGDLN TKLMTRLVED FSEAVGSSMR YTCLNSEKEF ERAICDMKMA VNNGDLSCSY DHSKWGPTMS PALF LSFLH TLELKNPRDR TKVNLEPVMN ILKWHLHKVV EVPINVAEAY CVGKLKRSLG LMGCDCTSVG EEFFHQYLQS RDQVP SHIM SVLDMGQGIL HNTSDLYGLI TEQFLCYALD LLYDVIPVTY TSSDDQVSLI KIPCLSDEKC QDRTELLEMV CFHEFL SSK LNKFISPKSV IGTFVAEFKS RFFVMGEETP LLTKFVSAAL HNVKCKTPTQ LSETIDTICD QCIANGVSTH IVSKISI RV NQLIRYSGYR ETPFGAIEEQ DVKDWVDGSR GYRLQRKIEA IFSDDKETMF IRNCARKVFN DIKRGKIFEE NLINLISR G GDEALSGFLQ YAGCSEDEIR QTLDYRWVNL ASFGDLRLVL RTKLMTSRRV LEKEEMPTLI KTIQSRLSRN FTKGVKKIL AESINKSAFQ SSVASGFIGF CKSMGSKCVR DGKGGFLYIK DIFTRIIPCL CGICERKPKV IYCQKSLQEV NQFSKPILWD YFSLVLTNA CELGEWVFSA VKSPQAPLVL CNKNFFWAVK PKAVRQIEDQ LGMNHVLHSI RRNYPKLFEE HLAPFMNDLQ V NRSLDSGR LKFLDVCVAL DMMNENLGII SHLLKVRDNN VYIVKQSDCA SAHVRQSEYT NWEVGISPQQ VCRNFMVQVV LS SMINPLV MSTSCLKSFF WFNEVLDLED DSQVDLAELT DFTLSIKNNK VSRAMFVEDI AMGYVVSSFD NIKVFLESVS VDN ISLLPQ EDMMDLHTVL RNVACQEAVK LKLIIQVEHT RVSTKFKLRR KMVYSYTIVS SLRVDDVSTP ELELNVDTMS QCVS GSEGN HSLLDGALVI ASLPLFTGHE SFDLAGLFID AGYALTNDDN ILGHVKFNFG DFYSEISNKY AYDLIGPDNL GEPLV LKEG VFYRGNERLS TYRVELSGDV IVKAIGALED IDSVETLLSQ LWPYLKMTSQ TILFQQEDFV LIYDLHKEQL IRSLDK FGD WLEFSNFKVA FSRSLNDLLI SDPQGQFRLK GVTCRPLKHK VEIKDID

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Macromolecule #2: RING finger protein Z

MacromoleculeName: RING finger protein Z / type: protein_or_peptide / ID: 2
Details: matrix zinc binding protein of JUNV, which inactivates JUNV RNA polymerase
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Junin mammarenavirus
Molecular weightTheoretical: 10.542071 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
MGNCNGASKS NQPDSSRVTQ PAAEFRRVAH SSLYGRYNCK CCWFADTNLI TCNDHYLCLR CHQVMLRNSD LCNICWKPLP TTITVPVEP TAPPP

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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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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration0.8 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES
1.0 mMC9H16ClO6PTris(2-carboxyethyl)phosphine(TCEP)

Details: Solutions were made fresh.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
Details: Frozen sample preparation begins immediately after glow discharge
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Number images used: 362657
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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