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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 dataEbola virus nucleoprotein - RNA complex, full map
Sample
  • Complex: Ebola virus nucleoprotein bound to RNA
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
KeywordsRNA-binding / nucleoprotein / nucleocapsid / capsid / VIRAL PROTEIN-RNA complex
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 / Zaire ebolavirus (strain Mayinga-76) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKirchdoerfer RN / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
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.
History
DepositionFeb 1, 2019-
Header (metadata) releaseFeb 27, 2019-
Map releaseMay 1, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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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 modelsPDB-6nut
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0522.png

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)
AnnotationEbola virus nucleoprotein - RNA complex, full map
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

Histogram

Histogram (log scale)

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Half map: Ebola virus nucleoprotein - RNA complex, first half map

Fileemd_0522_half_map_1.map
AnnotationEbola virus nucleoprotein - RNA complex, first half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ebola virus nucleoprotein - RNA complex, second half map

Fileemd_0522_half_map_2.map
AnnotationEbola virus nucleoprotein - RNA complex, second half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ebola virus nucleoprotein bound to RNA

EntireName: Ebola virus nucleoprotein bound to RNA
Components
  • Complex: Ebola virus nucleoprotein bound to RNA
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')

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Supramolecule #1: Ebola virus nucleoprotein bound to RNA

SupramoleculeName: Ebola virus nucleoprotein bound to RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 177 kDa/nm

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76
Molecular weightTheoretical: 50.267098 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 PTDSQ

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') / type: rna / ID: 2
Details: The poly-adenosine sequence was modeled to represent the mixed identity of nucleotide sequences bound to nucleoprotein.
Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration3.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloridesodium chloride
1.0 mMCaCl2calcium chloride
5.0 mMbeta-mercaptoethanol2-Mercaptoethanol
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 47478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-65 / Number grids imaged: 1 / Number real images: 731 / Average exposure time: 13.0 sec. / Average electron dose: 49.7 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 24608 / Software - Name: RELION (ver. 2.1)
Startup modelType of model: INSILICO MODEL
In silico model: Bead model generated using estimated helical parameters derived from Bharat et al. PNAS 2012 and Sugita et al. Nature 2018.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 2.84 Å
Applied symmetry - Helical parameters - Δ&Phi: -14.71 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 24609
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4ztg

chain_id: A, residue_range: 37-361, source_name: PDB, initial_model_type: experimental model

5z9w

chain_id: A, residue_range: 20-400, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL
Output model

PDB-6nut:
Ebola virus nucleoprotein - RNA complex

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