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- EMDB-65447: Cryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase ... -

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Entry
Database: EMDB / ID: EMD-65447
TitleCryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase in complex with ERDRP-0519
Map data
Sample
  • Complex: Cryo-EM Structure of Peste Des Petits Ruminants 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 / complex / RNA / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / 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 ...GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / 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.
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciespeste-des-petits-ruminants virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 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_65447.png

Downloads & links

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Map

FileDownload / File: emd_65447.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.011988929 - 1.9175665
Average (Standard dev.)0.0022625884 (±0.036920507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 262.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65447_msk_1.map
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Half map: #2

Fileemd_65447_half_map_1.map
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Half map: #1

Fileemd_65447_half_map_2.map
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Sample components

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Entire : Cryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase ...

EntireName: Cryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase in complex with ERDRP-0519
Components
  • Complex: Cryo-EM Structure of Peste Des Petits Ruminants 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 Peste Des Petits Ruminants Virus Polymerase ...

SupramoleculeName: Cryo-EM Structure of Peste Des Petits Ruminants Virus Polymerase in complex with ERDRP-0519
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: peste-des-petits-ruminants virus

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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: peste-des-petits-ruminants virus
Molecular weightTheoretical: 247.576297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSLSVNQVL YPEVHLDSPI VTNKLVAILE YSGIDHNYVL EDQTLVKNIR YRLGCGFSNQ MIINNRGVGE TVNSKLKSYP HNRHIIYPD CNKELFCIKD SCISKKLSEL FKKGNSLYSK ISHQVLDCLK RVNGKLGLGT DLTYGLKEGI LDLGLHMHSS Q WFETFLFW ...String:
MDSLSVNQVL YPEVHLDSPI VTNKLVAILE YSGIDHNYVL EDQTLVKNIR YRLGCGFSNQ MIINNRGVGE TVNSKLKSYP HNRHIIYPD CNKELFCIKD SCISKKLSEL FKKGNSLYSK ISHQVLDCLK RVNGKLGLGT DLTYGLKEGI LDLGLHMHSS Q WFETFLFW FTIKTEMRSM IKEQSHICHK RRYNPIFVSG DAFEVLVSRD LVVIIDKNTQ YVFYLTFELV LMYCDVIEGR LM TETAMAI DQRYSELLSR VRYLWDLIDG FFPTLGNTTY QVVALLEPLS LAYLQLQDVT LELRGAFLDH CFKELYEILE HCG IDTEGT YNSITEGLDY VFITHDIHLT GEIFSFFRSF GHPRLEAVTA AENVRKHMNQ PKVISYETMM KGHAVFCGII INGF RDRHG GSWPPVALPE HASAAIRNAQ ASGEGLTHDL CIDNWKSFVG FKFGCFMPLS LDSDLTMYLK DKALAALKNE WDSVY PKEY LRYNPPRGTE SRRLVEVFLN DSSFDPYNMI MYVVNGSYLK DPEFNLSYSL KEKEIKETGR LFAKMTYKMR ACQVIA ENL ISNGVGKYFR DNGMAKDEHD LTKALHTLAV SGVPKNNKDN HRGGPPRRTT NREVRSSQDT KTQNRDKVQG GPVYNYL RC QPISPDQGES YETVSAFITA DLKKYCLNWR YETISIFAQR LNEIYGLPSF FQWLHRILEK SVLYVSDPHC PPDLDNHI P LDSVPNAQIF IKYPMGGIEG YCQKLWTIST IPYLYLAAYE SGVRIASLVQ GDNQTIAVTK RVPSSWPYSL KKREASKAA QNYFVVLRQR LHDVGHHLKA NETIVSSHFF VYSKGIYYDG LLVSQSLKSI ARCVFWSETI VDETRAACSN IATTVAKSIE RGYDRYLAY SLNILKIFQQ ILISLNFTIN TTMTQDVVAP IIENGDLLIR MALLPAPIGG LNYLNMSRLF VRNIGDPVTS S IADLKRMI DAGLMPEETL HQVMTQTPGE SSYLDWASDP YSANLPCVQS ITRLLKNITA RYILISSPNP MLKGLFHEGS RD EDEELAS FLMDRHIIVP RAAHEILDHS ITGAREAIAG MLDTTKGLIR TSMKRGGLTP RVLARLSNYD YEQFRSGITL LTK KGQCYL IDKDSCSVQL AIALRSHMWA RLARGRPIYG LEVPDILESM NGYLIKRHES CAICETGSSH YGWFFVPAGC QLDD VSRET SALRVPYVGS TTEERTDMKL AFVRSPSRSL KSAVRIATVY SWAYGDDEKS WGEAWMLARQ RANITLDELR MITPV STST NLAHRLRDRS TQVKYSGTSL VRVARYTTIS NDNLSFVISE KKVDTNFIYQ QGMLLGLGIL ENLFRLEATT GVSNTV LHL HVETECCVVP MVDHPRIPSL RNIKVTDELC TNPLIYDRSP IIEHDATRLY SQSHRRHLVE FVTWSTSQLY HILAKST AM SMIELITRFE KDHMNEIAAL IGDDDINSFI TEFLLVEPRL FIVYLGQCAA INWAFDIHYH RPSGKHQMGE LLYSLLSR M SKGVYKIFTN ALSHPKVYKK FWRSGVIEPI HGPSLDTQNL HVTVCDMIYG SYVTYLDLLL NDELDDYPYL LCESDEDVV TDRFDNIQAK HLCVLADVYC SSKRCPSIIG MSPIEKCTIL THYIKGESVQ SPSGTSWNTD PLVVDHYSCS LTYLRCGSIK QIRLRVDPG FVFEALTDVD FKQPRKAKLD ISVVGLTDFS PPCDNVGDFL GTINTLRHNL PVTGTGVSNY EVHAYRRIGL N SSACYKAV EISTLIRPSL EVGEHGLFLG EGSGSMLAAY KEVLKLANCY YNSGVTAEGR AGQREISPYP SEMSLVENQM GI ERSVKVL FNGKPEVTWV GTTDCYKYII SNIQTSSLGF IHSDIETLPT KDAVEKLEEF ASILSLSLIL GKIGSITVVK VMP ISGDFT QGFIAYAIQY FRESLLAYPR YSNFISTECY LIMIGLKANR LINPEAIKQS IIRAGVRTAP GLVSHILSGK QKGC IQSFL GDPYIQGDFN KHLKSLTPIE KILVNCGLSI NGTKICRDLI HHDIASGPDG LMSSTIILYR ELAHFKDNIR SQHGM FHPY PVLANSRQRE LILRIAKKFW GYVLLYSDDP ALIRQTIKNL KRNHLTFDLH SNPFIKGLSK AEKLLVRTSS LRREWL FTL DTKEVKEWFK LVGYSALIRG

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: peste-des-petits-ruminants virus
Molecular weightTheoretical: 54.85759 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEEQAYHVN KGLECIKSLK ASPPDLSTIR DTIESWREGL SPSGRATPNP DTSEGDHQSI NQSCSPAIGP NKVYLSPGDN LGFREITGN DCEAGLGGVQ GKRSNSQVQR YYVYSHGGEE IEGLEDADSL VVQADPPVAN VFNGGEDGSD DSDVDSGPDD P SRDTLYDR ...String:
MAEEQAYHVN KGLECIKSLK ASPPDLSTIR DTIESWREGL SPSGRATPNP DTSEGDHQSI NQSCSPAIGP NKVYLSPGDN LGFREITGN DCEAGLGGVQ GKRSNSQVQR YYVYSHGGEE IEGLEDADSL VVQADPPVAN VFNGGEDGSD DSDVDSGPDD P SRDTLYDR GSVAGNDVAR STDVEKLEGA DIQEVLNSQK GKGGRFQGGK TLRVPEIPDV KHSRPSAQSI KKGTDGNSVS SG TVTECLS ISGATQAVPE SRWESSEQNA SVGSVLKSAR SAETIQGLTQ ESGTIASLTQ PKENDSEYEY EDDLFKEIQD IRA SIAKIH DDNKTILSKL DSILLLKGEV DTIKKQISKQ NISISTIEGH LSSIMIAIPG FGKDIKDPTS EVELNPDLRP IISR DSGRA LAEVLKKPAV DRSQKIGTKA NSSSKGQLLK DLQLKPVDKQ ASSAIGFVPS DHESSRNVIR SIIKSSKLNT DHKDY LLDL LNDVKGSKDL KEFHKMLTAI LAKHP

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: 300 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 3880076
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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