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- EMDB-0522: Ebola virus nucleoprotein - RNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0522
TitleEbola virus nucleoprotein - RNA complex
Map data
SampleEbola virus nucleoprotein bound to RNA:
Nucleoprotein / nucleic-acidNucleic acid
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / Nucleoprotein
Function and homology information
SourceEbola virus - Mayinga, Zaire, 1976 / Zaire ebolavirus (strain Mayinga-76) / Human (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKirchdoerfer RN / Ward AB
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex.
Authors: Robert N Kirchdoerfer / Erica Ollmann Saphire / Andrew B Ward /
Abstract: Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The ...Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1 Å resolution single-particle cryo-electron microscopy structure of the nucleoprotein-RNA helical filament presented here resembles previous structures determined at lower resolution, while providing improved molecular details of protein-protein and protein-RNA interactions. The higher resolution of the structure presented here will facilitate the design and characterization of novel and specific Ebola virus therapeutics targeting the nucleocapsid.
Validation ReportPDB-ID: 6nut

SummaryFull reportAbout validation report
DateDeposition: Feb 1, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: May 1, 2019 / Update: May 8, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nut
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6nut
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0522.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 360 pix.
= 414. Å
1.15 Å/pix.
x 360 pix.
= 414. Å
1.15 Å/pix.
x 360 pix.
= 414. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.100345664 - 0.18299763
Average (Standard dev.)0.0018217752 (±0.010993032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1000.1830.002

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Supplemental data

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Mask #1

Fileemd_0522_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Ebola virus nucleoprotein bound to RNA

EntireName: Ebola virus nucleoprotein bound to RNA / Number of components: 3

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Component #1: protein, Ebola virus nucleoprotein bound to RNA

ProteinName: Ebola virus nucleoprotein bound to RNA / Recombinant expression: No
MassTheoretical: 177 MDa
SourceSpecies: Ebola virus - Mayinga, Zaire, 1976
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: 293F

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Component #2: protein, Nucleoprotein

ProteinName: Nucleoprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.267098 kDa
SourceSpecies: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: nucleic-acid, RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')

nucleic acidName: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') / Class: RNA
Details: The poly-adenosine sequence was modeled to represent the mixed identity of nucleotide sequences bound to nucleoprotein.
Structure: OTHER / Synthetic: No
Sequence:
AAAAAA
MassTheoretical: 1.930277 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 2.84 Å / Delta phi: -14.71 %deg;
Sample solutionSpecimen conc.: 3.8 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 49.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47478.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 731

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4ZTG, 5Z9W
Chain ID: A, A
Output model

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