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- EMDB-3871: The structure of Ebola virus nucleocapsid-like assemblies from re... -

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Basic information

Entry
Database: EMDB / ID: EMD-3871
TitleThe structure of Ebola virus nucleocapsid-like assemblies from recombinant virus-like particles (nucleoprotein, VP24,VP35,VP40)
Map dataSubtomogram averaging of nucleocapsid-like assembly formed from recombinantly expressed Ebola Nucleoprotein (NP), VP24, VP35, VP40.
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Membrane-associated protein VP24
Keywordsnucleocapsid / virus-like particle / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


suppression by virus of host intracellular interferon activity / suppression by virus of host cytokine production / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II ...suppression by virus of host intracellular interferon activity / suppression by virus of host cytokine production / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / viral RNA genome packaging / molecular sequestering activity / helical viral capsid / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral genome replication / viral budding from plasma membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / negative regulation of gene expression / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / membrane
Similarity search - Function
Filovirus membrane-associated VP24 / Filovirus membrane-associated protein VP24 / Ebola nucleoprotein / Ebola nucleoprotein / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile.
Similarity search - Domain/homology
Nucleoprotein / Polymerase cofactor VP35 / Membrane-associated protein VP24
Similarity search - Component
Biological speciesZaire ebolavirus (strain Mayinga-76) / Ebola virus - Mayinga, Zaire, 1976
Methodsubtomogram averaging / cryo EM / Resolution: 7.3 Å
AuthorsWan W / Kolesnikova L
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research CouncilERC-CoG-648432 MEMBRANEFUSION Germany
European Molecular Biology OrganizationALTF 748-2014 Germany
German Research FoundationSonderforschungsbereich 1021 Germany
CitationJournal: Nature / Year: 2017
Title: Structure and assembly of the Ebola virus nucleocapsid.
Authors: William Wan / Larissa Kolesnikova / Mairi Clarke / Alexander Koehler / Takeshi Noda / Stephan Becker / John A G Briggs /
Abstract: Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles ...Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.
History
DepositionSep 13, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseNov 8, 2017-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ehm
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ehm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3871.png

Downloads & links

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Map

FileDownload / File: emd_3871.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging of nucleocapsid-like assembly formed from recombinantly expressed Ebola Nucleoprotein (NP), VP24, VP35, VP40.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 192 pix.
= 341.76 Å		1.78 Å/pix.
x 192 pix.
= 341.76 Å		1.78 Å/pix.
x 192 pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-5.856038 - 10.570264
Average (Standard dev.)-0.03055102 (±0.9822338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 341.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z341.760341.760341.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-5.85610.570-0.031

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Supplemental data

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Sample components

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Entire : Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976
Components
  • Virus: Ebola virus - Mayinga, Zaire, 1976
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Membrane-associated protein VP24

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Supramolecule #1: Ebola virus - Mayinga, Zaire, 1976

SupramoleculeName: Ebola virus - Mayinga, Zaire, 1976 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed virus-like particles produced by expression of nucleoprotein, VP24, VP35, VP40.
NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 280.0 Å

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76
Molecular weightTheoretical: 83.3875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSRPQKIWM APSLTESDMD YHKILTAGLS VQQGIVRQRV IPVYQVNNLE EICQLIIQAF EAGVDFQESA DSFLLMLCLH HAYQGDYKL FLESGAVKYL EGHGFRFEVK KRDGVKRLEE LLPAVSSGKN IKRTLAAMPE EETTEANAGQ FLSFASLFLP K LVVGEKAC ...String:
MDSRPQKIWM APSLTESDMD YHKILTAGLS VQQGIVRQRV IPVYQVNNLE EICQLIIQAF EAGVDFQESA DSFLLMLCLH HAYQGDYKL FLESGAVKYL EGHGFRFEVK KRDGVKRLEE LLPAVSSGKN IKRTLAAMPE EETTEANAGQ FLSFASLFLP K LVVGEKAC LEKVQRQIQV HAEQGLIQYP TAWQSVGHMM VIFRLMRTNF LIKFLLIHQG MHMVAGHDAN DAVISNSVAQ AR FSGLLIV KTVLDHILQK TERGVRLHPL ARTAKVKNEV NSFKAALSSL AKHGEYAPFA RLLNLSGVNN LEHGLFPQLS AIA LGVATA HGSTLAGVNV GEQYQQLREA ATEAEKQLQQ YAESRELDHL GLDDQEKKIL MNFHQKKNEI SFQQTNAMVT LRKE RLAKL TEAITAASLP KTSGHYDDDD DIPFPGPIND DDNPGHQDDD PTDSQDTTIP DVVVDPDDGS YGEYQSYSEN GMNAP DDLV LFDLDEDDED TKPVPNRSTK GGQQKNSQKG QHIEGRQTQS RPIQNVPGPH RTIHHASAPL TDNDRRNEPS GSTSPR MLT PINEEADPLD DADDETSSLP PLESDDEEQD RDGTSNRTPT VAPPAPVYRD HSEKKELPQD EQQDQDHTQE ARNQDSD NT QSEHSFEEMY RHILRSQGPF DAVLYYHMMK DEPVVFSTSD GKEYTYPDSL EEEYPPWLTE KEAMNEENRF VTLDGQQF Y WPVMNHKNKF MAILQHHQ

UniProtKB: Nucleoprotein

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Macromolecule #2: Membrane-associated protein VP24

MacromoleculeName: Membrane-associated protein VP24 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76
Molecular weightTheoretical: 28.250811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKATGRYNL ISPKKDLEKG VVLSDLCNFL VSQTIQGWKV YWAGIEFDVT HKGMALLHRL KTNDFAPAWS MTRNLFPHLF QNPNSTIES PLWALRVILA AGIQDQLIDQ SLIEPLAGAL GLISDWLLTT NTNHFNMRTQ RVKEQLSLKM LSLIRSNILK F INKLDALH ...String:
MAKATGRYNL ISPKKDLEKG VVLSDLCNFL VSQTIQGWKV YWAGIEFDVT HKGMALLHRL KTNDFAPAWS MTRNLFPHLF QNPNSTIES PLWALRVILA AGIQDQLIDQ SLIEPLAGAL GLISDWLLTT NTNHFNMRTQ RVKEQLSLKM LSLIRSNILK F INKLDALH VVNYNGLLSS IEIGTQNHTI IITRTNMGFL VELQEPDKSA MNRMKPGPAK FSLLHESTLK AFTQGSSTRM QS LILEFNS SLAI

UniProtKB: Membrane-associated protein VP24

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
0.1 mMEDTAethylenediaminetetraacetic acid
50.0 mMTris-HCltrisaminomethane hydrochloride
GridModel: C-flat 2/1 3C / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3708 pixel / Digitization - Frames/image: 1-5 / Average exposure time: 2.3 sec. / Average electron dose: 3.4 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: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFrames were aligned using K2Align software, based off the MotionCorr algorithm. Tomograms were reconstructed with IMOD, using stripwise CTF-correction and weighted back projection. Subtomogram averaging was performed using scripts derived from TOM, AV3, and DYNAMO.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: AV3
Details: Local resolution was estimated using moving window FSC calculations. Resolution varies from 7.3 to 15.2 Angstroms.
Number subtomograms used: 1
ExtractionNumber tomograms: 63 / Number images used: 379428 / Reference model: None
Software:
Namedetails
Amira (ver. 4)placing spline points
TOM Toolboxsubtomogram extraction

Details: Points along the helical axis were manually placed to define a spline. A cylindrical grid as defined at a given radius from the spline; grid spacing was chosen to provide ~4x oversampling.
Final angle assignmentType: OTHER / Software - Name: AV3
Details: Iterative angular search was performed via maximization of a modified constrained cross-correlation function.

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Atomic model buiding 1

DetailsNucleoprotein model from Ebola virus nucleoprotein 1-450 was first rigid body fitted into the inner nucleoprotein densities. Densities were then subtracted, and VP24 pdb was then fit into remaining densities. All models were rigid-body fitted using UCSF Chimera.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6ehm:
Model of the Ebola virus nucleocapsid subunit from recombinant virus-like particles

PDB-8ust:
In-virion structure of Ebola virus nucleocapsid-like assemblies from recombinant virus-like particles (nucleoprotein, VP24,VP35,VP40)

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