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- EMDB-62461: Polymerase complex-inhibitor IERDRP-0519-bound measles virus L-P ... -

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Basic information

Entry
Database: EMDB / ID: EMD-62461
TitlePolymerase complex-inhibitor IERDRP-0519-bound measles virus L-P complex
Map data
Sample
  • Complex: Polymerase complex
    • 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
KeywordsComplex / Transcription
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / 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 / 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 ...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 / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciesMeasles virus strain Ichinose-B95a
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang YR / Zhang HQ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2025
Title: Structures of the measles virus polymerase complex with non-nucleoside inhibitors and mechanism of inhibition.
Authors: Yiru Wang / Lixia Zhao / Yi Zhang / Xiuxia Gao / Yannan Wang / Wenping Shi / Roger D Kornberg / Heqiao Zhang /
Abstract: The measles virus (MeV), a highly contagious non-segmented negative-sense RNA virus in the Paramyxoviridae family, causes millions of infections annually, with no approved antivirals available. The ...The measles virus (MeV), a highly contagious non-segmented negative-sense RNA virus in the Paramyxoviridae family, causes millions of infections annually, with no approved antivirals available. The viral polymerase complex, comprising the large (L) protein and the tetrameric phosphoprotein (P), is a key antiviral target. We determined the cryo-electron microscopy structures of the MeV polymerase complex alone and bound to two non-nucleoside inhibitors, ERDRP-0519 and AS-136A. Inhibitor binding induces a conformational change in the catalytic loop, allosterically locking the polymerase in an inactive "GDN-out" state. These findings led to the proposal that ERDRP-0519 would also be effective against Nipah virus (NiV), a highly pathogenic virus with no available antivirals. This proposal was confirmed by structure determination of the NiV polymerase complex and by inhibition of transcription.
History
DepositionNov 19, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_62461.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 280 pix.
= 270.004 Å
0.96 Å/pix.
x 280 pix.
= 270.004 Å
0.96 Å/pix.
x 280 pix.
= 270.004 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9643 Å
Density
Contour LevelBy AUTHOR: 0.0459
Minimum - Maximum-0.29999065 - 0.53206146
Average (Standard dev.)0.0004440362 (±0.014438917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 270.004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62461_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_62461_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Sample components

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Entire : Polymerase complex

EntireName: Polymerase complex
Components
  • Complex: Polymerase complex
    • 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: Polymerase complex

SupramoleculeName: Polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Measles virus strain Ichinose-B95a

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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 virus strain Ichinose-B95a
Molecular weightTheoretical: 248.056953 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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: 3 / Enantiomer: LEVO
Source (natural)Organism: Measles virus strain Ichinose-B95a
Molecular weightTheoretical: 53.961113 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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: 2 / 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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111194
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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