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- EMDB-6903: Ebola virus nucleoprotein-RNA complex -

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Basic information

Entry
Database: EMDB / ID: 6903
TitleEbola virus nucleoprotein-RNA complex
Map dataEbolavirus nucleoprotein RNA complex (biological assembly)
SampleEbolavirus nucleoprotein RNA complex (biological assembly)
  • Ebolavirus nucleoprotein (residues 19-406)
  • nucleic-acidNucleic acid
SourceEbola virus - Mayinga, Zaire, 1976 / Homo sapiens (human) / synthetic construct (others)
Methodhelical reconstruction / cryo EM / 3.6 Å resolution
AuthorsSugita Y / Matsunami H / Kawaoka Y / Noda T / Wolf M
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
Validation ReportPDB-ID: 5z9w

SummaryFull reportAbout validation report
DateDeposition: Feb 5, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 24, 2018 / Last update: Nov 14, 2018

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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
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  • 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 models: PDB-5z9w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6903.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.39 Å/pix.
= 417. Å
300 pix
1.39 Å/pix.
= 417. Å
300 pix
1.39 Å/pix.
= 417. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-6.9264145 - 14.411011999999999
Average (Standard dev.)0.000000002842075 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 417.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-6.92614.4110.000

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Supplemental data

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Sample components

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Entire Ebolavirus nucleoprotein RNA complex (biological assembly)

EntireName: Ebolavirus nucleoprotein RNA complex (biological assembly)
Number of components: 3

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Component #1: protein, Ebolavirus nucleoprotein RNA complex (biological assembly)

ProteinName: Ebolavirus nucleoprotein RNA complex (biological assembly)
Recombinant expression: No
MassTheoretical: 166 kDa
SourceSpecies: Ebola virus - Mayinga, Zaire, 1976
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #2: protein, Ebolavirus nucleoprotein (residues 19-406)

ProteinName: Ebolavirus nucleoprotein (residues 19-406) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.496086 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: nucleic-acid, RNA (6-MER)

Nucleic-acidName: RNA (6-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUU
MassTheoretical: 1.792037 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.8
Support filmGatan Solarus
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 100 % / Details: 3 second blot, 2.5uL.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 105 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal), 47619.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 4000.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 77.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2467 / Sampling size: 5 microns
Details: frame alignment and dose weighting using motioncor2

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Image processing

ProcessingMethod: helical reconstruction
Details: frame alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: deconvolution in RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: RELION
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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