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- EMDB-71613: Cryo-EM structure of the respiratory syncytial virus polymerase (... -

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Entry
Database: EMDB / ID: EMD-71613
TitleCryo-EM structure of the respiratory syncytial virus polymerase (L:P) in pre-translocation elongation state
Map data
Sample
  • Complex: Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in pre-translocation elongation state
    • Complex: respiratory syncytial virus polymerase
      • Protein or peptide: RNA-directed RNA polymerase L
      • Protein or peptide: Phosphoprotein
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*CP*GP*A)-3')
      • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')
KeywordsRespiratory syncytial virus / RNA-dependent RNA polymerase / nucleotide addition cycle / VIRAL PROTEIN-RNA complex / VIRAL PROTEIN / TRANSFERASE-RNA complex
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / ATP binding / metal ion binding
Similarity search - Function
Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase ...Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesRespiratory syncytial virus A2 / Respiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsCao D / Chen Z / Gao Y / Roesler C / Gooneratne I / Liang B
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130950 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116788 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129539 United States
Simons FoundationSF349247 United States
CitationJournal: Nat Commun / Year: 2026
Title: Orchestrated and dynamic nucleotide addition cycle during respiratory syncytial virus early-stage elongation.
Authors: Dongdong Cao / Zhenhang Chen / Yunrong Gao / Claire Roesler / Inesh Gooneratne / Cristopher Mera / Lisa Zhuang / Julia Slack / Elijah Nudell-Cook / Jenny Vy / Jasmine Berry / Maurice Royal / ...Authors: Dongdong Cao / Zhenhang Chen / Yunrong Gao / Claire Roesler / Inesh Gooneratne / Cristopher Mera / Lisa Zhuang / Julia Slack / Elijah Nudell-Cook / Jenny Vy / Jasmine Berry / Maurice Royal / Masthan Shaik / Ryan Youngs / Bo Liang /
Abstract: The respiratory syncytial virus (RSV) polymerase (L:P complex) is responsible for viral RNA transcription and replication, where nucleotide addition cycles (NACs) are executed repeatedly during ...The respiratory syncytial virus (RSV) polymerase (L:P complex) is responsible for viral RNA transcription and replication, where nucleotide addition cycles (NACs) are executed repeatedly during elongation in both processes. Using cryo-EM, we capture snapshots of RSV polymerase in action during early-stage elongation and in four distinct NAC states: NTP-bound, pre-reaction, pre-translocation, and post-translocation. Strikingly, we observe all five domains of RSV L in NTP-bound and post-translocation states. In contrast, only two domains are visible in pre-reaction and pre-translocation states, similar to previously reported apo or promoter-bound structures. Importantly, these snapshots reveal the synergistic and dynamic interaction networks among key residues and motifs of RSV polymerase, RNA template, product, incoming nucleotide, and metal ions across NAC states. Our findings provide the first comprehensive insights into orchestrated macro-domain rearrangements and micro-motif changes of RSV polymerase during NAC catalysis, facilitating antiviral therapeutics targeting RSV and related nonsegmented negative-sense RNA viruses, including rabies, Nipah, and Ebola.
History
DepositionJul 6, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71613.png

Downloads & links

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Map

FileDownload / File: emd_71613.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 207.104 Å		1.08 Å/pix.
x 192 pix.
= 207.104 Å		1.08 Å/pix.
x 192 pix.
= 207.104 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07867 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.264003 - 1.7713237
Average (Standard dev.)0.0004709765 (±0.07677176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 207.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71613_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71613_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the respiratory syncytial virus polymerase (...

EntireName: Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in pre-translocation elongation state
Components
  • Complex: Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in pre-translocation elongation state
    • Complex: respiratory syncytial virus polymerase
      • Protein or peptide: RNA-directed RNA polymerase L
      • Protein or peptide: Phosphoprotein
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*CP*GP*A)-3')
      • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')

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Supramolecule #1: Cryo-EM structure of the respiratory syncytial virus polymerase (...

SupramoleculeName: Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in pre-translocation elongation state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: respiratory syncytial virus polymerase

SupramoleculeName: respiratory syncytial virus polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Respiratory syncytial virus A2

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Respiratory syncytial virus A2 / Synthetically produced: Yes

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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: Respiratory syncytial virus / Strain: A2
Molecular weightTheoretical: 250.704484 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 STNLAGHWIL IIQLMKDSKG IFEKDWGE G YITDHMFINL KVFFNAYKTY LLCFHKGYGK AKLECDMNTS DLLCVLELID SSYWKSMSKV FLEQKVIKYI LSQDASLHR VKGCHSFKLW FLKRLNVAEF TVCPWVVNID YHPTHMKAIL TYIDLVRMGL INIDRIHIKN KHKFNDEFYT SNLFYINYNF SDNTHLLTK HIRIANSELE NNYNKLYHPT PETLENILAN PIKSNDKKTL NDYCIGKNVD SIMLPLLSNK KLIKSSAMIR T NYSKQDLY NLFPMVVIDR IIDHSGNTAK SNQLYTTTSH QISLVHNSTS LYCMLPWHHI NRFNFVFSST GCKISIEYIL KD LKIKDPN CIAFIGEGAG NLLLRTVVEL HPDIRYIYRS LKDCNDHSLP IEFLRLYNGH INIDYGENLT IPATDATNNI HWS YLHIKF AEPISLFVCD AELSVTVNWS KIIIEWSKHV RKCKYCSSVN KCMLIVKYHA QDDIDFKLDN ITILKTYVCL GSKL KGSEV YLVLTIGPAN IFPVFNVVQN AKLILSRTKN FIMPKKADKE SIDANIKSLI PFLCYPITKK GINTALSKLK SVVSG DILS YSIAGRNEVF SNKLINHKHM NILKWFNHVL NFRSTELNYN HLYMVESTYP YLSELLNSLT TNELKKLIKI TGSLLY NFH NE

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus / Strain: A2
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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Macromolecule #3: RNA (5'-R(P*AP*CP*GP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*CP*GP*A)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 1.263842 KDa
SequenceString:
ACGA

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Macromolecule #4: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 3.666104 KDa
SequenceString:
UUUUUUUCUC GU

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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

Concentration0.35 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8snx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 34951
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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