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- EMDB-65364: Cryo-EM structure of the human measles virus RNA-dependent RNA po... -

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Basic information

Entry
Database: EMDB / ID: EMD-65364
TitleCryo-EM structure of the human measles virus RNA-dependent RNA polymerase complex bound to viral protein C
Map data
Sample
  • Complex: Measles virus RNA-dependent RNA polymerase complex bound to viral protein C
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Phosphoprotein
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L,Strep II and FLAG tag
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Protein C,Green fluorescent protein
  • Ligand: ZINC ION
  • Ligand: water
KeywordsMeasles virus RNA-dependent RNA polymerase complex bound to viral protein C / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / host cell cytoplasmic vesicle / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...GDP polyribonucleotidyltransferase / host cell cytoplasmic vesicle / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / viral genome replication / bioluminescence / cell chemotaxis / generation of precursor metabolites and energy / virion component / outer membrane-bounded periplasmic space / host cell cytoplasm / periplasmic space / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / DNA damage response / DNA-templated transcription / host cell nucleus / RNA binding / ATP binding / membrane
Similarity search - Function
Paramyxoviridae nonstructural protein C / Non-structural protein C / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal ...Paramyxoviridae nonstructural protein C / Non-structural protein C / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / 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. / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Phosphoprotein / RNA-directed RNA polymerase L / Protein C / Green fluorescent protein
Similarity search - Component
Biological speciesMeasles virus genotype A-vaccine / synthetic construct (others) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsDu T / Wang J / Wu S / Ru H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371344 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural insights into measles virus RNA synthesis regulation and pan-paramyxoviral polymerase inhibition by ERDRP-0519.
Authors: Tianjiao Du / Jiening Wang / Chengji Yang / Rubing Xue / Ying Chen / Kaiyue Jie / Xiaokang Zhang / Long Zhang / Gaojie Song / Qiansen Zhang / Shan Wu / Heng Ru /
Abstract: Nonsegmented negative-sense RNA viruses (nsNSVs) rely on a multifunctional RNA-dependent RNA polymerase (RdRP) complex for transcription and replication. In measles virus (MeV), the nonstructural ...Nonsegmented negative-sense RNA viruses (nsNSVs) rely on a multifunctional RNA-dependent RNA polymerase (RdRP) complex for transcription and replication. In measles virus (MeV), the nonstructural protein C has long been implicated in regulating RNA synthesis, yet its precise role remains unclear. Here, we show that the MeV C protein directly associates with the RdRP complex. Using cryoelectron microscopy, we determined atomic-resolution structures of the MeV polymerase with and without C, revealing that C binding stabilizes the C-terminal region of L and locks the complex into a replication-competent elongation state. Biochemical data further show that C promotes N protein recruitment, enhancing polymerase processivity through facilitating encapsidation during replication. Additionally, we also resolved high-resolution structures of MeV and Nipah virus (NiV) polymerases bound to ERDRP-0519, an orally available morbillivirus inhibitor. Unexpectedly, the compound occupies an allosteric pocket within the RdRp domain rather than the previously predicted PRNTase domain, overlapping conserved resistance sites. This binding induces conformational changes in palm subdomain, blocking RNA template and nucleotide engagement, thereby halting RNA synthesis. These findings uncover distinct regulatory and inhibitory mechanisms in paramyxovirus polymerases and provide a structural framework for the rational design of broad-spectrum antivirals targeting MeV, NiV, and potentially other clinically relevant nsNSVs.
History
DepositionJul 13, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65364.png

Downloads & links

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Map

FileDownload / File: emd_65364.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306.36 Å		0.85 Å/pix.
x 360 pix.
= 306.36 Å		0.85 Å/pix.
x 360 pix.
= 306.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-1.3615878 - 1.852684
Average (Standard dev.)-0.000056627516 (±0.037849706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65364_msk_1.map
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Half map: #2

Fileemd_65364_half_map_1.map
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Half map: #1

Fileemd_65364_half_map_2.map
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Sample components

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Entire : Measles virus RNA-dependent RNA polymerase complex bound to viral...

EntireName: Measles virus RNA-dependent RNA polymerase complex bound to viral protein C
Components
  • Complex: Measles virus RNA-dependent RNA polymerase complex bound to viral protein C
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Phosphoprotein
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L,Strep II and FLAG tag
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Protein C,Green fluorescent protein
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Measles virus RNA-dependent RNA polymerase complex bound to viral...

SupramoleculeName: Measles virus RNA-dependent RNA polymerase complex bound to viral protein C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Measles virus genotype A-vaccine
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Phosphoprotein

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Phosphoprotein
type: protein_or_peptide / ID: 1
Details: N-terminal MBP tag, 3C cleavage site,Sequence reference for Measles virus genotype A-vaccine is not available at the time of biocuration. Current sequence reference is from UniProt id P35974.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Measles virus genotype A-vaccine
Molecular weightTheoretical: 66.334383 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF ...String:
MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NG PWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYE EELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTGTDYDIPT TLEVLFQGPL GSGD YYDDE LFSDVQDIKT ALAKIHEDNQ KIISKLESLL LLKGEVESIK KQINRQNISI STLEGHLSSI MIAIPGLGKD PNDPT ADVE INPDLKPIIG RDSGRALAEV LKKPVASRQL QGMTNGRTSS RGQLLKEFQP KPIGKKMSSA VGFVPDTGPA SRSVIR SII KSSRLEEDRK RYLMTLLDDI KGANDLAKFH QMLMKIIMK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Phosphoprotein

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,RNA-directed RNA polymerase L,Strep II and FLAG tag
type: protein_or_peptide / ID: 2
Details: N terminal HisMBP tag, 3C cleavage site, TEV cleavage site, C-terminal Strep II and FLAG tag,Sequence reference for Measles virus genotype A-vaccine is not available at the time of ...Details: N terminal HisMBP tag, 3C cleavage site, TEV cleavage site, C-terminal Strep II and FLAG tag,Sequence reference for Measles virus genotype A-vaccine is not available at the time of biocuration. Current sequence reference is from UniProt id P35975.
Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 297.006906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF ...String:
MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NG PWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYE EELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTGTDYDIPT TLEVLFQGPL GSMD SLSVN QILYPEVHLD SPIVTNKIVA ILEYARVPHA YSLEDPTLCQ NIKHRLKNGF SNQMIINNVE VGNVIKSKLR SYPAH SHIP YPNCNQDLFN IEDKESTRKI RELLKKGNSL YSKVSDKVFQ CLRDTNSRLG LGSELREDIK EKVINLGVYM HSSQWF EPF LFWFTVKTEM RSVIKSQTHT CHRRRHTPVF FTGSSVELLI SRDLVAIISK ESQHVYYLTF ELVLMYCDVI EGRLMTE TA MTIDARYTEL LGRVRYMWKL IDGFFPALGN PTYQIVAMLE PLSLAYLQLR DITVELRGAF LNHCFTEIHD VLDQNGFS D EGTYHELIEA LDYIFITDDI HLTGEIFSFF RSFGHPRLEA VTAAENVRKY MNQPKVIVYE TLMKGHAIFC GIIINGYRD RHGGSWPPLT LPLHAADTIR NAQASGEGLT HEQCVDNWKS FAGVKFGCFM PLSLDSDLTM YLKDKALAAL QREWDSVYPK EFLRYDPPK GTGSRRLVDV FLNDSSFDPY DVIMYVVSGA YLHDPEFNLS YSLKEKEIKE TGRLFAKMTY KMRACQVIAE N LISNGIGK YFKDNGMAKD EHDLTKALHT LAVSGVPKDL KESHRGGPVL KTYSRSPVHT STRNVRAAKG FIGFPQVIRQ DQ DTDHPEN MEAYETVSAF ITTDLKKYCL NWRYETISLF AQRLNEIYGL PSFFQWLHKR LETSVLYVSD PHCPPDLDAH IPL YKVPND QIFIKYPMGG IEGYCQKLWT ISTIPYLYLA AYESGVRIAS LVQGDNQTIA VTKRVPSTWP YNLKKREAAR VTRD YFVIL RQRLHDIGHH LKANETIVSS HFFVYSKGIY YDGLLVSQSL KSIARCVFWS ETIVDETRAA CSNIATTMAK SIERG YDRY LAYSLNVLKV IQQILISLGF TINSTMTRDV VIPLLTNNDL LIRMALLPAP IGGMNYLNMS RLFVRNIGDP VTSSIA DLK RMILASLMPE ETLHQVMTQQ PGDSSFLDWA SDPYSANLVC VQSITRLLKN ITARFVLIHS PNPMLKGLFH DDSKEED EG LAAFLMDRHI IVPRAAHEIL DHSVTGARES IAGMLDTTKG LIRASMRKGG LTSRVITRLS NYDYEQFRAG MVLLTGRK R NVLIDKESCS VQLARALRSH MWARLARGRP IYGLEVPDVL ESMRGHLIRR HETCVICECG SVNYGWFFVP SGCQLDDID KETSSLRVPY IGSTTDERTD MKLAFVRAPS RSLRSAVRIA TVYSWAYGDD DSSWNEAWLL ARQRANVSLE ELRVITPIST STNLAHRLR DRSTQVKYSG TSLVRVARYT TISNDNLSFV ISDKKVDTNF IYQQGMLLGL GVLETLFRLE KDTGSSNTVL H LHVETDCC VIPMIDHPRI PSSRKLELRA ELCTNPLIYD NAPLIDRDTT RLYTQSHRRH LVEFVTWSTP QLYHILAKST AL SMIDLVT KFEKDHMNEI SALIGDDDIN SFITEFLVIE PRLFTIYLGQ CAAINWAFDV HYHRPSGKYQ MGELLSSFLS RMS KGVFKV LVNALSHPKI YKKFWHCGII EPIHGPSLDA QNLHTTVCNM VYTCYMTYLD LLLNEELEEF TFLLCESDED VVPD RFDNI QAKHLCVLAD LYCQPGACPP IRGLRPVEKC AVLTDHIKAE ARLSPAGSSW NINPIIVDHY SCSLTYLRRG SIKQI RLRV DPGFIFDALA EVNVSQPKIG SNNISNMSIK AFRPPHDDVA KLLKDINTSK HNLPISGGNL ANYEIHAFRR IGLNSS ACY KAVEISTLIR RCLEPGEDGL FLGEGSGSML ITYKEILKLN KCFYNSGVSA NSRSGQRELA PYPSEVGLVE HRMGVGN IV KVLFNGRPEV TWVGSVDCFN FIVSNIPTSS VGFIHSDIET LPNKDTIEKL EELAAILSMA LLLGKIGSIL VIKLMPFS G DFVQGFISYV GSYYREVNLV YPRYSNFIST ESYLVMTDLK ANRLMNPEKI KQQIIESSVR TSPGLIGHIL SIKQLSCIQ AIVGDVVSRG DINPTLKKLT PIEQVLINCG LAINGPKLCK ELIHHDVASG QDGLLNSILI LYRELARFKD NRRSQQGMFH AYPVLVSSR QRELISRITR KFWGHILLYS GNRKLINKFI QNLKSGYLIL DLHQNIFVKN LSKSEKQIIM TGGLKREWVF K VTVKETKE WYKLVGYSAL IKDSRENLYF QGSGWSHPQF EKGGGSGGGS GGSAWSHPQF EKGSDYKDDD DK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, RNA-directed RNA polymerase L

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Macromolecule #3: Maltose/maltodextrin-binding periplasmic protein,Protein C,Green ...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Protein C,Green fluorescent protein
type: protein_or_peptide / ID: 3
Details: N-terminal HisMBP tag, 3C cleavage site, TEV cleavage site, C-terminal GFP and FLAG tag,Sequence reference for Measles virus genotype A-vaccine is not available at the time of biocuration. ...Details: N-terminal HisMBP tag, 3C cleavage site, TEV cleavage site, C-terminal GFP and FLAG tag,Sequence reference for Measles virus genotype A-vaccine is not available at the time of biocuration. Current sequence reference is from UniProt id P35977.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 94.418805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF ...String:
MGSSHHHHHH GTKTEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSAL M FNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NG PWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK SYE EELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTGTDYDIPT TLEVLFQGPL GSMS KTDWN ASGLSRPSPS AHWPSRKLWQ HGQKYQTTQD RSEPPAGKRR QAVRVSANHA SQQLDQLKAV HLASAVRDLE RAMTT LKLW ESPQEISRHQ ALGYSVIMFM ITAVKRLRES KMLTLSWFNQ ALMVIAPYQE ETMNLKTAMW ILANLIPRDM LSLTGD LLP SLWGSGLLML KLQKEGRSTS SSRENLYFQG NGSSGSMVSK GEELFTGVVP ILVELDGDVN GHKFSVSGEG EGDATYG KL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKQHD FFKSAMPEGY VQERTIFFKD DGNYKTRAEV KFEGDTLV N RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI KVNFKIRHNI EDGSVQLADH YQQNTPIGDG PVLLPDNHY LSTQSKLSKD PNEKRDHMVL LEFVTAAGIT LGMDELYKDY KDDDDK

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Protein C, Green fluorescent protein

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.2 mg/mL
BufferpH: 7.5 / Details: 300mM NaCl, 25mM HEPES, 1mM TCEP, 6mM MgCl2
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.52 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 591603
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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