[English] 日本語
Yorodumi
- EMDB-65366: Cryo-EM structure of the human measles virus RNA-dependent RNA po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65366
TitleCryo-EM structure of the human measles virus RNA-dependent RNA polymerase complex
Map data
Sample
  • Complex: Measles virus RNA-dependent RNA polymerase complex
    • 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
  • Ligand: ZINC ION
KeywordsMeasles virus RNA-dependent RNA polymerase complex / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / 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 ...GDP polyribonucleotidyltransferase / 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 / cell chemotaxis / 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 / RNA binding / ATP binding / membrane
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. / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesMeasles virus genotype A-vaccine / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 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

-
Structure visualization

Supplemental images

emd_65366.png

Downloads & links

-
Map

FileDownload / File: emd_65366.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-1.1009793 - 1.4255266
Average (Standard dev.)-0.0002299398 (±0.0353179)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65366_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65366_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65366_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Measles virus RNA-dependent RNA polymerase complex

EntireName: Measles virus RNA-dependent RNA polymerase complex
Components
  • Complex: Measles virus RNA-dependent RNA polymerase complex
    • 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
  • Ligand: ZINC ION

-
Supramolecule #1: Measles virus RNA-dependent RNA polymerase complex

SupramoleculeName: Measles virus RNA-dependent RNA polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Measles virus genotype A-vaccine
Molecular weightTheoretical: 560 KDa

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

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Phosphoprotein
type: protein_or_peptide / ID: 1
Details: N-terminal HisMBP 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

-
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

-
Macromolecule #3: ZINC ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.5 / Details: 150mM NaCl, 25mM HEPES, 1mM TCEP, 6mM MgCl2
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse.

-
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123051
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
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