[English] 日本語
Yorodumi
- EMDB-37130: Cryo-EM structure of the human parainfluenza virus hPIV3 L-P poly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37130
TitleCryo-EM structure of the human parainfluenza virus hPIV3 L-P polymerase in dimeric form
Map dataCryo-EM map of the human parainfluenza virus hPIV3 L-P polymerase in dimeric form, class 1
Sample
  • Complex: Human parainfluenza virus hPIV3 L-P polymerase in dimeric form
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Keywordsdimeric polymerase / parainfluenza virus / L-P polymerase / cryo-EM structure / non-segmented negative-strand RNA virus / L-L dimerization / RNA replication / RdRp active site / 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-dependent 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-dependent RNA polymerase activity / GTPase activity / DNA-templated transcription / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Paramyxovirinae P phosphoprotein C-terminal domain / Paramyxovirinae P phosphoprotein C-terminal region / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / RNA-directed RNA polymerase, paramyxovirus / 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 ...Paramyxovirinae P phosphoprotein C-terminal domain / Paramyxovirinae P phosphoprotein C-terminal region / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / RNA-directed RNA polymerase, paramyxovirus / 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.
Similarity search - Domain/homology
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesHuman respirovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsXie J / Wang L / Zhai G / Wu D / Lin Z / Wang M / Yan X / Gao L / Huang X / Fearns R / Chen S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for dimerization of a paramyxovirus polymerase complex.
Authors: Jin Xie / Mohamed Ouizougun-Oubari / Li Wang / Guanglei Zhai / Daitze Wu / Zhaohu Lin / Manfu Wang / Barbara Ludeke / Xiaodong Yan / Tobias Nilsson / Lu Gao / Xinyi Huang / Rachel Fearns / Shuai Chen /
Abstract: The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a ...The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a cofactor protein, such as phosphoprotein (P). Previous studies have shown that the nsNSV polymerase can adopt a dimeric form, however, the structure of the dimer and its function are poorly understood. Here we determine a 2.7 Å cryo-EM structure of human parainfluenza virus type 3 (hPIV3) L-P complex with the connector domain (CD') of a second L built, while reconstruction of the rest of the second L-P obtains a low-resolution map of the ring-like L core region. This study reveals detailed atomic features of nsNSV polymerase active site and distinct conformation of hPIV3 L with a unique β-strand latch. Furthermore, we report the structural basis of L-L dimerization, with CD' located at the putative template entry of the adjoining L. Disruption of the L-L interface causes a defect in RNA replication that can be overcome by complementation, demonstrating that L dimerization is necessary for hPIV3 genome replication. These findings provide further insight into how nsNSV polymerases perform their functions, and suggest a new avenue for rational drug design.
History
DepositionAug 9, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37130.png

Downloads & links

-
Map

FileDownload / File: emd_37130.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the human parainfluenza virus hPIV3 L-P polymerase in dimeric form, class 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0225
Minimum - Maximum-0.059882548 - 0.13835108
Average (Standard dev.)0.000024363715 (±0.0028735108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_37130_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half1 map

Fileemd_37130_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map

Fileemd_37130_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human parainfluenza virus hPIV3 L-P polymerase in dimeric form

EntireName: Human parainfluenza virus hPIV3 L-P polymerase in dimeric form
Components
  • Complex: Human parainfluenza virus hPIV3 L-P polymerase in dimeric form
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

-
Supramolecule #1: Human parainfluenza virus hPIV3 L-P polymerase in dimeric form

SupramoleculeName: Human parainfluenza virus hPIV3 L-P polymerase in dimeric form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human respirovirus 3

-
Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Details: NP_067153.2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 260.103703 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MISNQQSDNG QKENIKNLGA KRARKMDTES NNGTVSDILY PECHLNSPIV KGKIAQLHTI MSLPQPYDMD DDSILVITRQ KIKLNKLDK RQRSIRRLKL ILTEKVNDLG KYTFIRYPEM SKEMFKLYIP GINSKVTELL LKADRTYSQM TDGLRDLWIN V LSKLASKN ...String:
MISNQQSDNG QKENIKNLGA KRARKMDTES NNGTVSDILY PECHLNSPIV KGKIAQLHTI MSLPQPYDMD DDSILVITRQ KIKLNKLDK RQRSIRRLKL ILTEKVNDLG KYTFIRYPEM SKEMFKLYIP GINSKVTELL LKADRTYSQM TDGLRDLWIN V LSKLASKN DGSNYDLNEE INNISKVHTT YKSDKWYNPF KTWFTIKYDM RRLQKARNEI TFNVGKDYNL LEDQKNFLLI HP ELVLILD KQNYNGYLIT PELVLMYCDV VEGRWNISAC AKLDPKLQSM YQKGNNLWEV IDKLFPIMGE KTFDVISLLE PLA LSLIQT HDPVKQLRGA FLNHVLSEME LIFESGESIR EFLSVDYIDK ILDIFNESTI DEIAEIFSFF RTFGHPPLEA SIAA EKVRK YMYIEKQLKF DTVNKCHAIF CTIIINGYRE RHGGQWPPVT LPDHAHEFII NAYGSNSAIS YENAVDYYQS FIGIK FNKF IEPQLDEDLT IYMKDKALSP KKSNWDTVYP ASNLLYRTNA SNESRRLVEV FIADSKFDPH QILDYVESGD WLDDPE FNI SYSLKEKEIK QEGRLFAKMT YKMRATQVLS ETLLANNIGK FFQENGMVKG EIELLKRLTT ISISGVPRYN EVYNNSK SH TDDLKTYNKI SNLNLSSNQK SKKFEFKSTD IYNDGYETVS CFLTTDLKKY CLNWRYESTA LFGETCNQIF GLNKLFNW L HPRLEGSTIY VGDPYCPPSD KEHISLEDHP DSGFYVHNPR GGIEGFCQKL WTLISISAIH LAAVRIGVRV TAMVQGDNQ AIAVTTRVPN NYDYRIKKEI VYKDVVRFFD SLREVMDDLG HELKLNETII SSKMFIYSKR IYYDGRILPQ ALKALSRCVF WSETVIDET RSASSNLATS FAKAIENGYS PVLGYACSIF KNIQQLYIAL GMNINPTITQ NIKDQYFKNS NWMQYASLIP A SVGGFNYM AMSRCFVRNI GDPSVAALAD IKRFIKANLL DRSVLYRIMN QEPGESSFLD WASDPYSCNL PQSQNITTMI KN ITARNVL QDSPNPLLSG LFTNTMIEED EELAEFLMDR KVILPRVAHD ILDNSLTGIR NAIAGMLDTT KSLIRVGINR GGL TYSLLR KISNYDLVQY ETLSRTLRLI VSDKIRYEDM CSVDLAIALR QKMWIHLSGG RMISGLETPD PLELLSGVVI TGSE HCKIC YSSDGTNPYT WMYLPGNIKI GSAETGVSSL RVPYFGSVTD ERSEAQLGYI KNLSKPAKAA IRIAMIYTWA FGNDE ISWM EASQIAQTRA NFTLDSLKIL TPVATSTNLS HRLKDTATQM KFSSTSLIRV SRFITMSNDN MSIKEANETK DTNLIY QQI MLTGLSVFEY LFRLKETTGH NPIVMHLHIE DECCIKESFN DEHINPESTL ELIRYPESNE FIYDKDPLKD VDLSKLM VI KDHSYTIDMN YWDDTDIIHA ISICTAITIA DTMSQLDRDN LKEIIVIAND DDINSLITEF LTLDILVFLK TFGGLLVN Q FAYTLYSLKI EGRDLIWDYI MRTLRDTSHS ILKVLSNALS HPKVFKRFWD CGVLNPIYGP NTASQDQIKL ALSICEYAL DLFMREWLNG VSLEIYICDS DMEVANDRKQ AFISRHLSFV CCLAEIASFG PNLLNLTYLE RLDLLKQYLE LNIKEDPTLK YVQISGLLI KSFPSTVTYV RKTAIKYLRI RGISPPEVID DWDPIEDENM LDNIVKTIND NCNKDNKGNK INNFWGLALK N YQVLKIRS ITSDSDDNDR LDASTSGLTL PQGGNYLSHQ LRLFGINSTS CLKALELSQI LMKEVNKDKD RLFLGEGAGA ML ACYDATL GPAINYYNSG LNITDVIGQR ELKIFPSEVS LVGKKLGNVT QILNRVKVLF NGNPNSTWIG NMECESLIWS ELN DKSIGL VHCDMEGAIG KSEETVLHEH YSVIRITYLI GDDDVVLVSK IIPTITPNWS RILYLYKLYW KDVSIISLKT SNPA STELY LISKDAYCTI MEPSEVVLSK LKRLSLLEEN NLLKWIILSK KRNNEWLHHE IKEGERDYGV MRPYHMALQI FGFQI NLNH LAKEFLSTPD LTNINNIIQS FQRTIKDVLF EWINITHDDK RHKLGGRYNI FPLKNKGKLR LLSRRLVLSW ISLSLS TRL LTGRFPDEKF EHRAQTGYVS LADTDLESLK LLSKNIIKNY RECIGSISYW FLTKEVKILM KLIGGAKLLG IPRQYKE PE EQLLENYNQH DEFDIDDYKD DDDK

UniProtKB: RNA-directed RNA polymerase L

-
Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2 / Details: NP_067149.1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human respirovirus 3
Molecular weightTheoretical: 68.471312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MESDAKNYQI MDSWEEESRD KSTNISSALN IIEFILSTDP QEDLSENDTI NTRTQQLSAT IYQPKIKPTE TSEKDSGSTD KNRQSGSSH ECTTEAKDRT IDQETVQRGP GRRSSSDSRA ETVVSGGISR SITNSKNGTQ NTEDIDLNEI RKMDKDSIEG K VRQSADVP ...String:
MESDAKNYQI MDSWEEESRD KSTNISSALN IIEFILSTDP QEDLSENDTI NTRTQQLSAT IYQPKIKPTE TSEKDSGSTD KNRQSGSSH ECTTEAKDRT IDQETVQRGP GRRSSSDSRA ETVVSGGISR SITNSKNGTQ NTEDIDLNEI RKMDKDSIEG K VRQSADVP SEISGSDVIF TTEQSRNSDH GRSLESISTP DTRSISVVTA ATPDDEEEIL MKNSRTKKSS SIHQEDDKRI KK GGKGKDW FKKSKDTDNQ IPTSDYRSTS KGQKKISKTT TINTDTKGQT EIQTESSGTQ SSSWNLTIDN NTDRTEQTNT TPP TTTSGS TYTKESIRTN SGSKPKTQKT NGKERKDTEE SNRFTERAIT LLQNLGVIQS TSKLDLYQDK RVVCVANVLN NVDT ASKID FLAGLVIGVS MDNDTKLTQI QNEMLNLKAD LKKMDESHRR LIENQREQLS LITSLISNLK IMTERGGKKD QNESN ERVS MIKTKLKEEK IKKTRFDPLM ETQGIDKNIP DLYRHAGNTL ENDVQVKSEI LSSYNESNAT RLIPKKVSST MRSLVA VIS NSNLSQSTKQ SYINELKHCK NDEEVSELMD MFNEDVNNCQ HHHHHH

UniProtKB: Phosphoprotein

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing #1

Image processing ID1
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102956
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
Image processing #2

Image processing ID2
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102956
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
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