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- EMDB-65444: Cryo-EM Structure of Measles Virus Polymerase in complex with ERD... -

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Entry
Database: EMDB / ID: EMD-65444
TitleCryo-EM Structure of Measles Virus Polymerase in complex with ERDRP-0519
Map data
Sample
  • Complex: Cryo-EM Structure of Measles Virus Polymerase in complex with ERDRP-0519
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
  • Ligand: 2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl]sulfonylphenyl]-5-(trifluoromethyl)pyrazole-3-carboxamide
KeywordsPolymerase / inhibitor / nipah virus / complex / REPLICATION
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / DNA-templated transcription ...GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
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 ...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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciesMeasles morbillivirus / Measles virus genotype B3
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsXue L / Gui J / Chang T / Pan H / Xiong X
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400116 to L.X China
National Natural Science Foundation of China (NSFC)82341085 to X.X China
CitationJournal: Cell / Year: 2026
Title: Differential inhibition of Morbillivirus and Henipavirus polymerases by ERDRP-0519 and structure-guided inhibitor optimization.
Authors: Lu Xue / Jiacheng Gui / Shenghua Gao / Xiaoxiao Gao / Tiancai Chang / Hainei Pan / Jielin Tang / Mingxia Zhang / Zimu Li / Binqian Zou / Heyu Zhao / Longyu Wang / Mei Li / Lijun Rong / ...Authors: Lu Xue / Jiacheng Gui / Shenghua Gao / Xiaoxiao Gao / Tiancai Chang / Hainei Pan / Jielin Tang / Mingxia Zhang / Zimu Li / Binqian Zou / Heyu Zhao / Longyu Wang / Mei Li / Lijun Rong / Richard K Plemper / Xinwen Chen / Jun He / Rongjuan Pei / Peng Zhan / Xiaoli Xiong /
Abstract: ERDRP-0519 is a non-nucleoside polymerase inhibitor developed against measles virus (MeV) of the Morbillivirus genus. Here, we show that ERDRP-0519 also cross-inhibits Nipah virus (NiV) of the ...ERDRP-0519 is a non-nucleoside polymerase inhibitor developed against measles virus (MeV) of the Morbillivirus genus. Here, we show that ERDRP-0519 also cross-inhibits Nipah virus (NiV) of the Henipavirus genus with reduced potency. ERDRP-0519 binds to a shared pocket within the RNA-dependent RNA polymerase (RdRp) palm domains of MeV, peste des petits ruminants virus (PPRV), and NiV polymerases. ERDRP-0519 forms more extensive interactions with Morbillivirus polymerases, whereas binding to NiV polymerase requires substantial RdRp motif rearrangements, likely incurring an energetic cost and resulting in reduced affinity. ERDRP-0519 binding impedes RNA synthesis by sterically blocking RNA and nucleotide binding. Guided by these insights, we designed GL22 and G671, ERDRP-0519 derivatives with extended moieties that engage additional cross-domain RdRp contacts in the NiV polymerase. These derivatives exert more extensive steric hindrance to RNA and nucleotide binding, enhancing biochemical inhibition potency. These findings elucidate the molecular mechanism of ERDRP-0519 action and guide structure-based inhibitor design.
History
DepositionJul 20, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65444.png

Downloads & links

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Map

FileDownload / File: emd_65444.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 416 pix.
= 394.202 Å		0.95 Å/pix.
x 416 pix.
= 394.202 Å		0.95 Å/pix.
x 416 pix.
= 394.202 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9476 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.0017546369 - 1.687882
Average (Standard dev.)0.000364096 (±0.013785095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 394.2016 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65444_msk_1.map
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Half map: #2

Fileemd_65444_half_map_1.map
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Half map: #1

Fileemd_65444_half_map_2.map
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Sample components

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Entire : Cryo-EM Structure of Measles Virus Polymerase in complex with ERD...

EntireName: Cryo-EM Structure of Measles Virus Polymerase in complex with ERDRP-0519
Components
  • Complex: Cryo-EM Structure of Measles Virus Polymerase in complex with ERDRP-0519
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
  • Ligand: 2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl]sulfonylphenyl]-5-(trifluoromethyl)pyrazole-3-carboxamide

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Supramolecule #1: Cryo-EM Structure of Measles Virus Polymerase in complex with ERD...

SupramoleculeName: Cryo-EM Structure of Measles Virus Polymerase in complex with ERDRP-0519
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Measles morbillivirus

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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: Measles morbillivirus
Molecular weightTheoretical: 248.056953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSLSVNQIL YPEVHLDSPI VTNKIVAILE YARVPHAYSL EDPTLCQNIK HRLKNGFSNQ MIINNVEVGN VIKSKLRSYP AHSHIPYPN CNQDLFNIED KESTRKIREL LKKGNSLYSK VSDKVFQCLR DTNSRLGLGS ELREDIKEKI INLGVYMHSS Q WFEPFLFW ...String:
MDSLSVNQIL YPEVHLDSPI VTNKIVAILE YARVPHAYSL EDPTLCQNIK HRLKNGFSNQ MIINNVEVGN VIKSKLRSYP AHSHIPYPN CNQDLFNIED KESTRKIREL LKKGNSLYSK VSDKVFQCLR DTNSRLGLGS ELREDIKEKI INLGVYMHSS Q WFEPFLFW FTVKTEMRSV IKSQTHTCHR RRHTPVFFTG SSVELLISRD LVAIISKESQ HVYYLTFELV LMYCDVIEGR LM TETAMTI DARYAELLGR VRYMWKLIDG FFPALGNPTY QIVAMLEPLS LAYLQLRDIT VELRGAFLNH CFTEIHDVLD QNG FSDEGT YHELIEALDY IFITDDIHLT GEIFSFFRSF GHPRLEAVTA AENVRKYMNQ PKVIVYETLM KGHAIFCGII INGY RDRHG GSWPPLTLPL HAADTIRNAQ ASGEGLTHEQ CVDNWKSFAG VRFGCFMPLS LDSDLTMYLK DKALAALQRE WDSVY PKEF LRYDPPKGTG SRRLVDVFLN DSSFDPYDMI MYVVSGAYLH DPEFNLSYSL KEKEIKETGR LFAKMTYKMR ACQVIA ENL ISNGIGKYFK DNGMAKDEHD LTKALHTLAV SGVPKDLKES HRGGPVLKTY SRSPVHTSTR NVKAEKGFVG FPHVIRQ NQ DTDHPENIET YETVSAFITT DLKKYCLNWR YETISLFAQR LNEIYGLPSF FQWLHKRLET SVLYVSDPHC PPDLDAHV P LCKVPNDQIF IKYPMGGIEG YCQKLWTIST IPYLYLAAYE SGVRIASLVQ GDNQTIAVTK RVPSTWPYNL KKREAARVT RDYFVILRQR LHDIGHHLKA NETIVSSHFF VYSKGIYYDG LLVSQSLKSI ARCVFWSETI VDETRAACSN IATTMAKSIE RGYDRYLAY SLNVLKVIQQ ILISLGFTIN STMTRDVVIP LLTNNDLLIR MALLPAPIGG MNYLNMSRLF VRNIGDPVTS S IADLKRMI LASLMPEETL HQVMTQQPGD SSFLDWASDP YSANLVCVQS ITRLLKNITA RFVLIHSPNP MLKGLFHDDS KE EDERLAA FLMDRHIIVP RAAHEILDHS VTGARESIAG MLDTTKGLIR ASMRKGGLTS RVITRLSNYD YEQFRAGMVL LTG RKRNVL IDKESCSVQL ARALRSHMWA RLARGRPIYG LEVPDVLESM RGHLIRRHET CVICECGSVN YGWFFVPSGC QLDD IDKET SSLRVPYIGS TTDERTDMKL AFVRAPSRSL RSAVRIATVY SWAYGDDDSS WNEAWLLARQ RANVSLEELR VITPI STST NLAHRLRDRS TQVKYSGTSL VRVARYTTIS NDNLSFVISD KKVDTNFIYQ QGMLLGLGVL ETLFRLEKDT GSSNTV LHL HVETDCCVIP MIDHPRIPSS RKLELRAELC TNPLIYDNAP LIDRDATRLY TQSHRRHLVE FVTWSTPQLY HILAKST AL SMIDLVTKFE KDHMNEISAL IGDDDINSFI TEFLLIEPRL FTIYLGQCAA INWAFDVHYH RPSGKYQMGE LLSSFLSR M SKGVFKVLVN ALSHPKIYKK FWHCGIIEPI HGPSLDAQNL HTTVCNMVYT CYMTYLDLLL NEELEEFTFL LCESDEDVV PDRFDNIQAK HLCVLADLYC QPGTCPPIRG LRPVEKCAVL TDHIKAEARL SPAGSSWNIN PIIVDHYSCS LTYLRRGSIK QIRLRVDPG FIFDALAEVN VSQPKVGSNN ISNMSIKDFR PPHDDVAKLL KDINTSKHNL PISGGSLANY EIHAFRRIGL N SSACYKAV EISTLIRRCL EPGEDGLFLG EGSGSMLITY KEILKLNKCF YNSGVSANSR SGQRELAPYP SEVGLVEHRM GV GNIVKVL FNGRPEVTWV GSIDCFNFIV SNIPTSSVGF IHSDIETLPN KDTIEKLEEL AAILSMALLL GKIGSILVIK LMP FSGDFV QGFISYVGSH YREVNLVYPR YSNFISTESY LVMTDLKANR LMNPEKIKQQ IIESSVRTSP GLIGHILSIK QLSC IQAIV GGAVSRGDIN PILKKLTPIE QVLISCGLAI NGPKLCKELI HHDVASGQDG LLNSILILYR ELARFKDNQR SQQGM FHAY PVLVSSRQRE LVSRITRKFW GHILLYSGNR KLINRFIQNL KSGYLVLDLH QNIFVKNLSK SEKQIIMTGG LKREWV FKV TVKETKEWYK LVGYSALIKD

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: Measles virus genotype B3
Molecular weightTheoretical: 53.961113 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEEQARHVK NGLECIRALK AEPIGSLAVE EAMAAWSEIS DNPGQDRATC KEEEAGSSGL SKPCLSAIGS TEGGAPRIRG QGSGESDDD AETLGIPSRN LQASSTGLQC YHVYDHSGEA VKGIQDADSI MVQSGLDGDS TLSGGDDESE NSDVDIGEPD T EGYAITDR ...String:
MAEEQARHVK NGLECIRALK AEPIGSLAVE EAMAAWSEIS DNPGQDRATC KEEEAGSSGL SKPCLSAIGS TEGGAPRIRG QGSGESDDD AETLGIPSRN LQASSTGLQC YHVYDHSGEA VKGIQDADSI MVQSGLDGDS TLSGGDDESE NSDVDIGEPD T EGYAITDR GSAPISMGFR ASDVETAEGG EIHELLKLQS RGNNFPKLGK TLNVPPPPNP SRASTSETPI KKGTDARLAS FG TEIASLL TGGATQCARK SPSEPSGPGA PAGNVPECVS NAALIQEWTP ESGTTISPRS QNNEEGGDYY DDELFSDVQD IKT ALAKIH EDNQKIISKL ESLLLLKGEV ESIKKQINRQ NISISTLEGH LSSIMIAIPG LGKDPNDPTA DVELNPDLKP IIGR DSGRA LAEVLKKPVA SRQLQGMTNG RTSSRGQLLK EFQLKPIGKK VSSAVGFVPD TGPASRSVIR SIIKSSRLEE DRKRY LMTL LDDIKGANDL AKFHQMLMKI IMK

UniProtKB: Phosphoprotein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: 2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl...

MacromoleculeName: 2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl]sulfonylphenyl]-5-(trifluoromethyl)pyrazole-3-carboxamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1EF9
Molecular weightTheoretical: 529.576 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 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: INSILICO MODEL
Final reconstructionNumber classes used: 148166 / Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2590005
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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