[English] 日本語
Yorodumi
- EMDB-62463: AS-136A-bound measles virus L-P complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62463
TitleAS-136A-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-piperidin-1-ylsulfonylphenyl)-5-(trifluoromethyl)pyrazole-3-carboxamide
KeywordsComplex / Transcription / AS-136A / Measles virus / L-P complex / polymerase complex
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 / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / 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 speciesParamyxoviridaeMeasles virus strain Ichinose-B95a / Measles virus strain Ichinose-B95a
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62463.png

Downloads & links

-
Map

FileDownload / File: emd_62463.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-1.1505085 - 1.4587728
Average (Standard dev.)-0.000048054662 (±0.028022345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62463_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62463_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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-piperidin-1-ylsulfonylphenyl)-5-(trifluoromethyl)pyrazole-3-carboxamide

-
Supramolecule #1: Polymerase complex

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

-
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

-
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

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: 2-methyl-~{N}-(4-piperidin-1-ylsulfonylphenyl)-5-(trifluoromethyl...

MacromoleculeName: 2-methyl-~{N}-(4-piperidin-1-ylsulfonylphenyl)-5-(trifluoromethyl)pyrazole-3-carboxamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1EGA
Molecular weightTheoretical: 416.418 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
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: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 126133
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more