[English] 日本語
Yorodumi
- EMDB-47176: Cryo-EM structure of the Measles Virus polymerase (L) protein in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47176
TitleCryo-EM structure of the Measles Virus polymerase (L) protein in complex with the tetrameric phosphoprotein (P)
Map dataCryo-EM map of the Measles virus L-P complex
Sample
  • Complex: The Measles virus L-P complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
KeywordsMeasles virus / L protein / phosphoprotein / RNA-dependent RNA polymerase / PRNTase / GDP polyribonucleotidyl transferase / RNA capping / MTase / viral replication / TRANSFERASE / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity ...GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / metal ion 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
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesMeasles virus strain Edmonston-B
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsLiu B / Wang D / Yang G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: The mechanochemical cycle of reactive full-length human dynein 1.
Authors: Pengxin Chai / Jun Yang / Indigo C Geohring / Steven M Markus / Yue Wang / Kai Zhang /
Abstract: Dynein-driven cargo transport has a pivotal role in diverse cellular activities, central to which is dynein's mechanochemical cycle. Here, we performed a systematic cryo-electron microscopic ...Dynein-driven cargo transport has a pivotal role in diverse cellular activities, central to which is dynein's mechanochemical cycle. Here, we performed a systematic cryo-electron microscopic investigation of the conformational landscape of full-length human dynein 1 in reaction, in various nucleotide conditions, on and off microtubules. Our approach reveals over 40 high-resolution structures, categorized into eight states, providing a dynamic and comprehensive view of dynein throughout its mechanochemical cycle. The described intermediate states reveal mechanistic insights into dynein function, including a 'backdoor' phosphate release model that coordinates linker straightening, how microtubule binding enhances adenosine triphosphatase activity through a two-way communication mechanism and the crosstalk mechanism between AAA1 and the regulatory AAA3 site. Our findings also lead to a revised model for the force-generating powerstroke and reveal means by which dynein exhibits unidirectional stepping. These results improve our understanding of dynein and provide a more complete model of its mechanochemical cycle.
History
DepositionOct 4, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47176.png

Downloads & links

-
Map

FileDownload / File: emd_47176.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the Measles virus L-P complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 384 pix.
= 339.968 Å		0.89 Å/pix.
x 384 pix.
= 339.968 Å		0.89 Å/pix.
x 384 pix.
= 339.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.02290388 - 1.7483463
Average (Standard dev.)0.00069409446 (±0.017389178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: The unsharpened cryo-EM map of the Measles virus L-P complex

Fileemd_47176_additional_1.map
AnnotationThe unsharpened cryo-EM map of the Measles virus L-P complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B of the Measles virus L-P complex

Fileemd_47176_half_map_1.map
AnnotationHalf map B of the Measles virus L-P complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A of the Measles virus L-P complex

Fileemd_47176_half_map_2.map
AnnotationHalf map A of the Measles virus L-P complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The Measles virus L-P complex

EntireName: The Measles virus L-P complex
Components
  • Complex: The Measles virus L-P complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein

-
Supramolecule #1: The Measles virus L-P complex

SupramoleculeName: The Measles virus L-P complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Measles virus strain Edmonston-B
Molecular weightTheoretical: 610 KDa

-
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 Edmonston-B
Molecular weightTheoretical: 247.910641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSLSVNQIL YPEVHLDSPI VTNKIVAILE YARVPHAYSL EDPTLCQNIK HRLKNGFSNQ MIINNVEVGN VIKSKLRSYP AHSHIPYPN CNQDLFNIED KESTRKIREL LKKGNSLYSK VSDKVFQCLR DTNSRLGLGS ELREDIKEKV INLGVYMHSS Q WFEPFLFW ...String:
MDSLSVNQIL YPEVHLDSPI VTNKIVAILE YARVPHAYSL EDPTLCQNIK HRLKNGFSNQ MIINNVEVGN VIKSKLRSYP AHSHIPYPN CNQDLFNIED KESTRKIREL LKKGNSLYSK VSDKVFQCLR DTNSRLGLGS ELREDIKEKV INLGVYMHSS Q WFEPFLFW FTVKTEMRSV IKSQTHTCHR RRHTPVFFTG SSVELLISRD LVAIISKESQ HVYYLTFELV LMYCDVIEGR LM TETAMTI DARYTELLGR VRYMWKLIDG FFPALGNPTY QIVAMLEPLS LAYLQLRDIT VELRGAFLNH CFTEIHDVLD QNG FSDEGT YHELIEALDY IFITDDIHLT GEIFSFFRSF GHPRLEAVTA AENVRKYMNQ PKVIVYETLM KGHAIFCGII INGY RDRHG GSWPPLTLPL HAADTIRNAQ ASGDGLTHEQ CVDNWKSFAG VKFGCFMPLS LDSDLTMYLK DKALAALQRE WDSVY PKEF LRYDPPKGTG SRRLVDVFLN DSSFDPYDVI MYVVSGAYLH DPEFNLSYSL KEKEIKETGR LFAKMTYKMR ACQVIA ENL ISNGIGKYFK DNGMAKDEHD LTKALHTLAV SGVPKDLKES HRGGPVLKTY SRSPVHTSTR NVRAAKGFIG FPQVIRQ DQ DTDHPENMEA YETVSAFITT DLKKYCLNWR YETISLFAQR LNEIYGLPSF FQWLHKRLET SVLYVSDPHC PPDLDAHI P LYKVPNDQIF 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 EDEGLAA 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 QPGTCPPIQG LRPVEKCAVL TDHIKAEAML SPAGSSWNIN PIIVDHYSCS LTYLRRGSIK QIRLRVDPG FIFDALAEVN VSQPKIGSNN ISNMSIKAFR PPHDDVAKLL KDINTSKHNL PISGGNLANY EIHAFRRIGL N SSACYKAV EISTLIRRCL EPGEDGLFLG EGSGSMLITY KEILKLSKCF YNSGVSANSR SGQRELAPYP SEVGLVEHRM GV GNIVKVL FNGRPEVTWV GSVDCFNFIV SNIPTSSVGF IHSDIETLPD KDTIEKLEEL AAILSMALLL GKIGSILVIK LMP FSGDFV QGFISYVGSH YREVNLVYPR YSNFISTESY LVMTDLKANR LMNPEKIKQQ IIESSVRTSP GLIGHILSIK QLSC IQAIV GDAVSRGDIN PTLKKLTPIE QVLINCGLAI NGPKLCKELI HHDVASGQDG LLNSILILYR ELARFKDNQR SQQGM FHAY PVLVSSRQRE LISRITRKFW GHILLYSGNR KLINKFIQNL KSGYLILDLH 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: 4 / Enantiomer: LEVO
Source (natural)Organism: Measles virus strain Edmonston-B
Molecular weightTheoretical: 54.088332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEEQARHVK NGLECIRALK AEPIGSLAIE EAMAAWSEIS DNPGQERATC REEKAGSSGL SKPCLSAIGS TEGGAPRIRG QGPGESDDD AETLGIPPRN LQASSTGLQC HYVYDHSGEA VKGIQDADSI MVQSGLDGDS TLSGGDNESE NSDVDIGEPD T EGYAITDR ...String:
MAEEQARHVK NGLECIRALK AEPIGSLAIE EAMAAWSEIS DNPGQERATC REEKAGSSGL SKPCLSAIGS TEGGAPRIRG QGPGESDDD AETLGIPPRN LQASSTGLQC HYVYDHSGEA VKGIQDADSI MVQSGLDGDS TLSGGDNESE NSDVDIGEPD T EGYAITDR GSAPISMGFR ASDVETAEGG EIHELLRLQS RGNNFPKLGK TLNVPPPPDP GRASTSGTPI KKGTDARLAS FG TEIASSL TGGATQCARK SPSEPSGPGA PAGNVPECVS NAALIQEWTP ESGTTISPRS QNNEEGGDHY DDELFSDVQD IKT ALAKIH EDNQKIISKL ESLLLLKGEV ESIKKQINRQ NISISTLEGH LSSIMIAIPG LGKDPNDPTA DVEINPDLKP IIGR DSGRA LAEVLKKPVA SRQLQGMTNG RTSSRGQLLK EFQLKPIGKK MSSAVGFVPD TGPASRSVIR SIIKSSRLEE DRKRY LMTL LDDIKGANDL AKFHQMLMKI IMKSG

UniProtKB: Phosphoprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Details: 50 mM Tris-HCl pH 8.0, 250 mM NaCl, 5% glycerol, 1 mM TCEP, and 4 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 63.0 K / Max: 77.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 17071 / Average exposure time: 1.7 sec. / Average electron dose: 54.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 8112589
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167313
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 75.98
Output model

PDB-9dus:
Cryo-EM structure of the Measles Virus polymerase (L) protein in complex with the tetrameric phosphoprotein (P)

+
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