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- EMDB-20754: Cryo-EM structure of the respiratory syncytial virus RNA polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-20754
TitleCryo-EM structure of the respiratory syncytial virus RNA polymerase
Map dataStructure of the respiratory syncytial virus RNA polymerase
Sample
  • Complex: the L protein of the human respiratory syncytial virus; the phosphoprotein (P) of human respiratory syncytial virus
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: the phosphoprotein (P) of human respiratory syncytial virus
KeywordsViral protein complexes / VIRAL PROTEIN / VIRAL PROTEIN-Transferase complex
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / virion component => GO:0044423 / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral life cycle / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / : / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / virion component => GO:0044423 / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral life cycle / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / : / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
RNA-directed RNA polymerase, paramyxovirus / Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase ...RNA-directed RNA polymerase, paramyxovirus / Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile.
Similarity search - Domain/homology
Phosphoprotein / RNA-directed RNA polymerase L / Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsCao D / Gao Y / Liang B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130950 United States
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of the respiratory syncytial virus RNA polymerase.
Authors: Dongdong Cao / Yunrong Gao / Claire Roesler / Samantha Rice / Paul D'Cunha / Lisa Zhuang / Julia Slack / Mason Domke / Anna Antonova / Sarah Romanelli / Shayon Keating / Gabriela Forero / ...Authors: Dongdong Cao / Yunrong Gao / Claire Roesler / Samantha Rice / Paul D'Cunha / Lisa Zhuang / Julia Slack / Mason Domke / Anna Antonova / Sarah Romanelli / Shayon Keating / Gabriela Forero / Puneet Juneja / Bo Liang /
Abstract: The respiratory syncytial virus (RSV) RNA polymerase, constituted of a 250 kDa large (L) protein and tetrameric phosphoprotein (P), catalyzes three distinct enzymatic activities - nucleotide ...The respiratory syncytial virus (RSV) RNA polymerase, constituted of a 250 kDa large (L) protein and tetrameric phosphoprotein (P), catalyzes three distinct enzymatic activities - nucleotide polymerization, cap addition, and cap methylation. How RSV L and P coordinate these activities is poorly understood. Here, we present a 3.67 Å cryo-EM structure of the RSV polymerase (L:P) complex. The structure reveals that the RNA dependent RNA polymerase (RdRp) and capping (Cap) domains of L interact with the oligomerization domain (P) and C-terminal domain (P) of a tetramer of P. The density of the methyltransferase (MT) domain of L and the N-terminal domain of P (P) is missing. Further analysis and comparison with other RNA polymerases at different stages suggest the structure we obtained is likely to be at an elongation-compatible stage. Together, these data provide enriched insights into the interrelationship, the inhibitors, and the evolutionary implications of the RSV polymerase.
History
DepositionSep 22, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseJan 22, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0463
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0463
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uen
  • Surface level: 0.0463
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20754.png

Downloads & links

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Map

FileDownload / File: emd_20754.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the respiratory syncytial virus RNA polymerase
Voxel sizeX=Y=Z: 1.63281 Å
Density
Contour LevelBy AUTHOR: 0.0463 / Movie #1: 0.0463
Minimum - Maximum-0.2648638 - 0.3498595
Average (Standard dev.)0.0001511138 (±0.014458609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 208.99968 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.63281251.63281251.6328125
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z209.000209.000209.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2650.3500.000

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Supplemental data

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Sample components

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Entire : the L protein of the human respiratory syncytial virus; the phosp...

EntireName: the L protein of the human respiratory syncytial virus; the phosphoprotein (P) of human respiratory syncytial virus
Components
  • Complex: the L protein of the human respiratory syncytial virus; the phosphoprotein (P) of human respiratory syncytial virus
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: the phosphoprotein (P) of human respiratory syncytial virus

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Supramolecule #1: the L protein of the human respiratory syncytial virus; the phosp...

SupramoleculeName: the L protein of the human respiratory syncytial virus; the phosphoprotein (P) of human respiratory syncytial virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respiratory syncytial virus
Molecular weightTheoretical: 360 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: Human respiratory syncytial virus
Molecular weightTheoretical: 173.586594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDPIINGNSA NVYLTDSYLK GVISFSECNA LGSYIFNGPY LKNDYTNLIS RQNPLIEHMN LKKLNITQSL ISKYHKGEIK LEEPTYFQS LLMTYKSMTS SEQIATTNLL KKIIRRAIEI SDVKVYAILN KLGLKEKDKI KSNNGQDEDN SVITTIIKDD I LSAVKDNQ ...String:
MDPIINGNSA NVYLTDSYLK GVISFSECNA LGSYIFNGPY LKNDYTNLIS RQNPLIEHMN LKKLNITQSL ISKYHKGEIK LEEPTYFQS LLMTYKSMTS SEQIATTNLL KKIIRRAIEI SDVKVYAILN KLGLKEKDKI KSNNGQDEDN SVITTIIKDD I LSAVKDNQ SHLKADKNHS TKQKDTIKTT LLKKLMCSMQ HPPSWLIHWF NLYTKLNNIL TQYRSNEVKN HGFTLIDNQT LS GFQFILN QYGCIVYHKE LKRITVTTYN QFLTWKDISL SRLNVCLITW ISNCLNTLNK SLGLRCGFNN VILTQLFLYG DCI LKLFHN EGFYIIKEVE GFIMSLILNI TEEDQFRKRF YNSMLNNITD AANKAQKNLL SRVCHTLLDK TVSDNIINGR WIIL LSKFL KLIKLAGDNN LNNLSELYFL FRIFGHPMVD ERQAMDAVKI NCNETKFYLL SSLSMLRGAF IYRIIKGFVN NYNRW PTLR NAIVLPLRWL TYYKLNTYPS LLELTERDLI VLSGLRFYRE FRLPKKVDLE MIINDKAISP PKNLIWTSFP RNYMPS HIQ NYIEHEKLKF SESDKSRRVL EYYLRDNKFN ECDLYNCVVN QSYLNNPNHV VSLTGKEREL SVGRMFAMQP GMFRQVQ IL AEKMIAENIL QFFPESLTRY GDLELQKILE LKAGISNKSN RYNDNYNNYI SKCSIITDLS KFNQAFRYET SCICSDVL D ELHGVQSLFS WLHLTIPHVT IICTYRHAPP YIGDHIVDLN NVDEQSGLYR YHMGGIEGWC QKLWTIEAIS LLDLISLKG KFSITALING DNQSIDISKP IRLMEGQTHA QADYLLALNS LKLLYKEYAG IGHKLKGTET YISRDMQFMS KTIQHNGVYY PASIKKVLR VGPWINTILD DFKVSLESIG SLTQELEYRG ESLLCSLIFR NVWLYNQIAL QLKNHALCNN KLYLDILKVL K HLKTFFNL DNIDTALTLY MNLPMLFGGG DPNLLYRSFY RRTPDFLTEA IVHSVFILSY YTNHDLKDKL QDLSDDRLNK FL TCIITFD KNPNAEFVTL MRDPQALGSE RQAKITSEIN RLAVTEVLST APNKIFSKSA QHYTTTEIDL NDIMQNIEPT YPH GLRVVY ESLPFYKAEK IVNLISGTKS ITNILEKTSA IDLTDIDRAT EMMRKNITLL IRILPLDCNR DKREILSMEN LSIT ELSKY VRERSWSLSN IVGVTSPSIM YTMDIKYTTS TISSGIIIEK YNVNSLTRGE RGPTKPWVGS STQEKKTMPV YNRQV LTKK QRDQIDLLAK LDWVYASIDN KDEFMEELSI GTLGLTYEKA KKLFPQYLSV NYLHRLTVSS RPCEFPASIP AYRTTN YHF DTSPINRILT EKYGDEDIDI VFQNCISFGL SLMSVVEQFT NVCPNRIILI PKLNEIHLMK PPIFTGDVDI HKLKQVI QK QHMFLPDKIS LTQYVELFLS NKTLKSGSHV NSNLILAHKI SDYFHNTYIL STNLAGHW

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: the phosphoprotein (P) of human respiratory syncytial virus

MacromoleculeName: the phosphoprotein (P) of human respiratory syncytial virus
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human respiratory syncytial virus
Molecular weightTheoretical: 27.165838 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEKFAPEFHG EDANNRATKF LESIKGKFTS PKDPKKKDSI ISVNSIDIEV TKESPITSNS TIINPTNETD DTAGNKPNYQ RKPLVSFKE DPTPSDNPFS KLYKETIETF DNNEEESSYS YEEINDQTND NITARLDRID EKLSEILGML HTLVVASAGP T SARDGIRD ...String:
MEKFAPEFHG EDANNRATKF LESIKGKFTS PKDPKKKDSI ISVNSIDIEV TKESPITSNS TIINPTNETD DTAGNKPNYQ RKPLVSFKE DPTPSDNPFS KLYKETIETF DNNEEESSYS YEEINDQTND NITARLDRID EKLSEILGML HTLVVASAGP T SARDGIRD AMVGLREEMI EKIRTEALMT NDRLEAMARL RNEESEKMAK DTSDEVSLNP TSEKLNNLLE GNDSDNDLSL ED F

UniProtKB: Phosphoprotein

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 91 %

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 253372

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6uen:
Cryo-EM structure of the respiratory syncytial virus RNA polymerase

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