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- EMDB-7343: Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit -

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Basic information

Entry
Database: EMDB / ID: EMD-7343
TitleEbola nucleoprotein nucleocapsid-like assembly and the asymmetric unit
Map dataEbola nucleoprotein nucleocapsid-like assembly
Sample
  • Complex: eNP nucleocapsid-like assembly
    • Protein or peptide: Nucleoprotein
KeywordsEbola / nucleoprotein / nucleocapsid / helical reconstruction / RNA BINDING PROTEIN
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
Methodhelical reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsSu Z / Wu C / Pintilie GD / Chiu W / Amarasinghe GK / Leung DW
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM12400701 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109664 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120943 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-16-1-0033 United States
CitationJournal: Cell Rep / Year: 2015
Title: An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.
Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / ...Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / Robert A Davey / Zbyszek Otwinowski / Christopher F Basler / Gaya K Amarasinghe /
Abstract: During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In ...During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
History
DepositionJan 13, 2018-
Header (metadata) releaseFeb 14, 2018-
Map releaseMar 7, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
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  • Surface view with fitted model
  • Atomic models: PDB-6c54
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6c54
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7343.png

Downloads & links

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Map

FileDownload / File: emd_7343.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEbola nucleoprotein nucleocapsid-like assembly
Voxel sizeX=Y=Z: 2.4 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.16373856 - 0.30754635
Average (Standard dev.)0.0022737961 (±0.0146839395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 633.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z633.600633.600633.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-288-288-288
NX/NY/NZ576576576
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.1640.3080.002

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Supplemental data

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Additional map: Ebola nucleoprotein asymmetric unit

Fileemd_7343_additional.map
AnnotationEbola nucleoprotein asymmetric unit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ebola nucleoprotein asymmetric unit

Fileemd_7343_additional_1.map
AnnotationEbola nucleoprotein asymmetric unit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : eNP nucleocapsid-like assembly

EntireName: eNP nucleocapsid-like assembly
Components
  • Complex: eNP nucleocapsid-like assembly
    • Protein or peptide: Nucleoprotein

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Supramolecule #1: eNP nucleocapsid-like assembly

SupramoleculeName: eNP nucleocapsid-like assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Zaire ebolavirus

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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
Molecular weightTheoretical: 48.14259 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LTAGLSVQQG IVRQRVIPVY QVNNLEEICQ LIIQAFEAGV DFQESADSFL LMLCLHHAYQ GDYKLFLESG AVKYLEGHGF RFEVKKRDG VKRLEELLPA VSSGKNIKRT LAAMPEEETT EANAGQFLSF ASLFLPKLVV GEKACLEKVQ RQIQVHAEQG L IQYPTAWQ ...String:
LTAGLSVQQG IVRQRVIPVY QVNNLEEICQ LIIQAFEAGV DFQESADSFL LMLCLHHAYQ GDYKLFLESG AVKYLEGHGF RFEVKKRDG VKRLEELLPA VSSGKNIKRT LAAMPEEETT EANAGQFLSF ASLFLPKLVV GEKACLEKVQ RQIQVHAEQG L IQYPTAWQ SVGHMMVIFR LMRTNFLIKF LLIHQGMHMV AGHDANDAVI SNSVAQARFS GLLIVKTVLD HILQKTERGV RL HPLARTA KVKNEVNSFK AALSSLAKHG EYAPFARLLN LSGVNNLEHG LFPQLSAIAL GVATAHGSTL AGVNVGEQYQ QLR EAATEA EKQLQQYAES RELDHLGLDD QEKKILMNFH QKKNEISFQQ TNAMVTLRKE RLAKLTEAIT AASLPKTSGH YDDD DDIPF PGPINDDDNP GHQDDDPTDS QDTTIPDV

UniProtKB: Nucleoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4 / Component - Concentration: 12.0 mM / Component - Formula: PBS / Component - Name: Phosphate-buffered saline / Details: 150 mM NaCl, 3 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.7 mm / Nominal magnification: 30000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 30 eV / Energy filter - Upper energy threshold: 30 eV
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 86.0 K / Max: 86.0 K
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: 2-32 / Number grids imaged: 2 / Number real images: 1266 / Average exposure time: 8.0 sec. / Average electron dose: 24.0 e/Å2

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Image processing

Segment selectionNumber selected: 200685
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2-beta)
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.65 Å
Applied symmetry - Helical parameters - Δ&Phi: -8.53 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2-beta) / Number images used: 169526

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 276 / Target criteria: Correlation coefficient
Output model

PDB-6c54:
Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit

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