[English] 日本語
Yorodumi
- EMDB-30129: Helical stem of the cleaved double-headed nucleocapsids of sendai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30129
TitleHelical stem of the cleaved double-headed nucleocapsids of sendai virus
Map datahelical stem of cleaved double-headed nucleocapsids
Sample
  • Complex: cleaved double-headed nucleocapsid of sendai virus
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
Keywordsnucleocapsid / Sendai virus / NUCLEAR PROTEIN / NUCLEAR PROTEIN-RNA complex
Function / homologyParamyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleoprotein
Function and homology information
Biological speciesMurine respirovirus / Sendai virus (strain Ohita) / synthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsShen Q / Shan H / Zhang N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870743 China
CitationJournal: Commun Biol / Year: 2021
Title: Structure and assembly of double-headed Sendai virus nucleocapsids.
Authors: Na Zhang / Hong Shan / Mingdong Liu / Tianhao Li / Rui Luo / Liuyan Yang / Lei Qi / Xiaofeng Chu / Xin Su / Rui Wang / Yunhui Liu / Wenzhi Sun / Qing-Tao Shen /
Abstract: Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins ...Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.
History
DepositionMar 18, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6m7d
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m7d
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30129.png

Downloads & links

-
Map

FileDownload / File: emd_30129.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhelical stem of cleaved double-headed nucleocapsids
Voxel sizeX=Y=Z: 0.52 Å
Density
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.084092945 - 0.12729745
Average (Standard dev.)0.0001875045 (±0.006377946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 270.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.520.520.52
M x/y/z520520520
origin x/y/z0.0000.0000.000
length x/y/z270.400270.400270.400
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS520520520
D min/max/mean-0.0840.1270.000

-
Supplemental data

-
Sample components

-
Entire : cleaved double-headed nucleocapsid of sendai virus

EntireName: cleaved double-headed nucleocapsid of sendai virus
Components
  • Complex: cleaved double-headed nucleocapsid of sendai virus
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

-
Supramolecule #1: cleaved double-headed nucleocapsid of sendai virus

SupramoleculeName: cleaved double-headed nucleocapsid of sendai virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Murine respirovirus

-
Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sendai virus (strain Ohita) / Strain: Ohita
Molecular weightTheoretical: 57.20002 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAGLLSTFDT FSSRRSESIN KSGGGAVIPG QRSTVSVFVL GPSVTDDADK LSIATTFLAH SLDTDKQHSQ RGGFLVSLLA MAYSSPELY LTTNGVNADV KYVIYNIEKD PKRTKTDGFI VKTRDMEYER TTEWLFGPMV NKSPLFQGQR DAADPDTLLQ I YGYPACLG ...String:
MAGLLSTFDT FSSRRSESIN KSGGGAVIPG QRSTVSVFVL GPSVTDDADK LSIATTFLAH SLDTDKQHSQ RGGFLVSLLA MAYSSPELY LTTNGVNADV KYVIYNIEKD PKRTKTDGFI VKTRDMEYER TTEWLFGPMV NKSPLFQGQR DAADPDTLLQ I YGYPACLG AIIVQVWIVL VKAITSSAGL RKGFFNRLEA FRQDGTVKGA LVFTGETVEG IGSVMRSQQS LVSLMVETLV TM NTARSDL TTLEKNIQIV GNYIRDAGLA SFMNTIKYGV ETKMAALTLS NLRPDINKLR SLIDTYLSKG PRAPFICILK DPV HGEFAP GNYPALWSYA MGVAVVQNKA MQQYVTGRTY LDMEMFLLGQ AVAKDAESKI SSALEDELGV TDTAKERLRH HLAN LSGGD GAYHKPTGGG AIEVALDNAD IDLEPEAHTD QDARGWGGDS GDRWARSMGS GHFITLHGAE RLEEETNDED VSDIE RRIA RRLAERRQED ATTHEDEGRN NGVDHDEEDD AAAAAGMGGI

UniProtKB: Nucleoprotein

-
Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Component:
ConcentrationFormula
20.0 mMTris
150.0 mMNaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.068 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.09 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.58 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134042
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
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://pdbjlvh1.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