[English] 日本語
Yorodumi
- EMDB-6903: Ebola virus nucleoprotein-RNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6903
TitleEbola virus nucleoprotein-RNA complex
Map dataEbolavirus nucleoprotein RNA complex (biological assembly)
Sample
  • Complex: Ebolavirus nucleoprotein RNA complex (biological assembly)
    • Protein or peptide: Ebolavirus nucleoprotein (residues 19-406)
    • RNA: RNA (6-MER)
Keywordsebolavirus / RNA / nucleoprotein / nucleocapsid / helical / VIRAL PROTEIN
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesEbola virus - Mayinga, Zaire, 1976 / Homo sapiens (human) / synthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSugita Y / Matsunami H / Kawaoka Y / Noda T / Wolf M
Funding support Japan, 9 items
OrganizationGrant numberCountry
the Ministry of Education, Culture, Science, Sports, and Technology26892028 Japan
Japan Science and Technology AgencyJPMJPR13L9 Japan
Japan Agency for Medical Research and Development17fk0108128h0001 Japan
the Ministry of Education, Culture, Science, Sports, and Technology16H06429 Japan
the Ministry of Education, Culture, Science, Sports, and Technology16K21723 Japan
the Ministry of Education, Culture, Science, Sports, and Technology16H06434 Japan
Japan Society for the Promotion of Science Japan
Daiichi Sankyo Foundation of Life Science Japan
Japan Agency for Medical Research and Development Japan
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution.
Authors: Yukihiko Sugita / Hideyuki Matsunami / Yoshihiro Kawaoka / Takeshi Noda / Matthias Wolf /
Abstract: Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain ...Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA. The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase. The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion. RNA binding and nucleoprotein oligomerization are synergistic and do not readily occur independently. Although recent cryo-electron tomography studies have revealed the overall architecture of the nucleocapsid core, there has been no high-resolution reconstruction of the nucleocapsid. Here we report the structure of a recombinant Ebola virus nucleoprotein-RNA complex expressed in mammalian cells without chemical fixation, at near-atomic resolution using single-particle cryo-electron microscopy. Our structure reveals how the Ebola virus nucleocapsid core encapsidates its viral genome, its sequence-independent coordination with RNA by nucleoprotein, and the dynamic transition between the RNA-free and RNA-bound states. It provides direct structural evidence for the role of the N terminus of nucleoprotein in subunit oligomerization, and for the hydrophobic and electrostatic interactions that lead to the formation of the helical assembly. The structure is validated as representative of the native biological assembly of the nucleocapsid core by consistent dimensions and symmetry with the full virion. The atomic model provides a detailed mechanistic basis for understanding nucleocapsid assembly and highlights key structural features that may serve as targets for anti-viral drug development.
History
DepositionFeb 5, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 24, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5z9w
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5z9w
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6903.png

Downloads & links

-
Map

FileDownload / File: emd_6903.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEbolavirus nucleoprotein RNA complex (biological assembly)
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-6.9264145 - 14.411011999999999
Average (Standard dev.)0.000000002842075 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 417.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z417.000417.000417.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-6.92614.4110.000

-
Supplemental data

-
Sample components

-
Entire : Ebolavirus nucleoprotein RNA complex (biological assembly)

EntireName: Ebolavirus nucleoprotein RNA complex (biological assembly)
Components
  • Complex: Ebolavirus nucleoprotein RNA complex (biological assembly)
    • Protein or peptide: Ebolavirus nucleoprotein (residues 19-406)
    • RNA: RNA (6-MER)

-
Supramolecule #1: Ebolavirus nucleoprotein RNA complex (biological assembly)

SupramoleculeName: Ebolavirus nucleoprotein RNA complex (biological assembly)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 166 KDa

-
Macromolecule #1: Ebolavirus nucleoprotein (residues 19-406)

MacromoleculeName: Ebolavirus nucleoprotein (residues 19-406) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.496086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYHKILTAG LSVQQGIVRQ RVIPVYQVNN LEEICQLIIQ AFEAGVDFQE SADSFLLMLC LHHAYQGDYK LFLESGAVKY LEGHGFRFE VKKRDGVKRL EELLPAVSSG KNIKRTLAAM PEEETTEANA GQFLSFASLF LPKLVVGEKA CLEKVQRQIQ V HAEQGLIQ ...String:
MDYHKILTAG LSVQQGIVRQ RVIPVYQVNN LEEICQLIIQ AFEAGVDFQE SADSFLLMLC LHHAYQGDYK LFLESGAVKY LEGHGFRFE VKKRDGVKRL EELLPAVSSG KNIKRTLAAM PEEETTEANA GQFLSFASLF LPKLVVGEKA CLEKVQRQIQ V HAEQGLIQ YPTAWQSVGH MMVIFRLMRT NFLIKFLLIH QGMHMVAGHD ANDAVISNSV AQARFSGLLI VKTVLDHILQ KT ERGVRLH PLARTAKVKN EVNSFKAALS SLAKHGEYAP FARLLNLSGV NNLEHGLFPQ LSAIALGVAT AHGSTLAGVN VGE QYQQLR EAATEAEKQL QQYAESRELD HLGLDDQEKK ILMNFHQKKN EISFQQTNAM VTLRKERLAK LT

-
Macromolecule #2: RNA (6-MER)

MacromoleculeName: RNA (6-MER) / 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 statehelical array

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMC4H12ClNO3Tris-HClTris
150.0 mMNaClSodium chloridesodium chloride
1.0 mMC10H12O8CaN2Na2x2H2OEDTAEthylenediaminetetraacetic acid
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 150 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 2.5uL.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 47619 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 100.0 K
Alignment procedureComa free - Residual tilt: 0.1 mrad
Detailsnanoprobe, parallel beam illumination
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-75 / Number grids imaged: 1 / Number real images: 2467 / Average exposure time: 15.0 sec. / Average electron dose: 105.0 e/Å2
Details: frame alignment and dose weighting using motioncor2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 232490 / Software - Name: EMAN2 (ver. 2.1) / Software - details: e2helixboxer.py
Startup modelType of model: OTHER / Details: cylinder created in SPIDER
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) / Details: RELION
Final reconstructionNumber classes used: 3 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 117552
Detailsframe alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5z9w:
Ebola virus nucleoprotein-RNA complex

+
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