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- EMDB-39081: Structure of the Ebola virus nucleocapsid subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-39081
TitleStructure of the Ebola virus nucleocapsid subunit
Map data
Sample
  • Virus: Zaire ebolavirus
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Membrane-associated protein VP24
    • RNA: RNA (12-MER)
KeywordsComplex / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


host cell endomembrane system / viral RNA genome packaging / helical viral capsid / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral budding from plasma membrane / 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 ...host cell endomembrane system / viral RNA genome packaging / helical viral capsid / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral budding from plasma membrane / 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 / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / membrane
Similarity search - Function
Filovirus membrane-associated VP24 / Filovirus membrane-associated protein VP24 / Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Nucleoprotein / Membrane-associated protein VP24
Similarity search - Component
Biological speciesZaire ebolavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsFujita-Fujiharu Y / Hu S / Hirabayashi A / Takamatsu Y / Ng Y / Houri K / Muramoto Y / Nakano M / Sugita Y / Noda T
Funding support Japan, 14 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21J12207 Japan
Japan Society for the Promotion of Science (JSPS)22KK0115 Japan
Japan Society for the Promotion of Science (JSPS)21K07059 Japan
Japan Society for the Promotion of Science (JSPS)22K19431 Japan
Japan Society for the Promotion of Science (JSPS)22KK0115 Japan
Japan Society for the Promotion of Science (JSPS)21K07052 Japan
Japan Science and TechnologyJPMJFR214S Japan
Japan Science and TechnologyJPMJCR20HA Japan
Japan Agency for Medical Research and Development (AMED)JP23fm0208101 Japan
Japan Agency for Medical Research and Development (AMED)JP22fm0208101 Japan
Japan Agency for Medical Research and Development (AMED)22wm0325023h9903 Japan
Japan Agency for Medical Research and Development (AMED)JP23fm0208101 Japan
Japan Agency for Medical Research and Development (AMED)22fk0108552h0001 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24.
Authors: Yoko Fujita-Fujiharu / Shangfan Hu / Ai Hirabayashi / Yuki Takamatsu / Yen Ni Ng / Kazuya Houri / Yukiko Muramoto / Masahiro Nakano / Yukihiko Sugita / Takeshi Noda /
Abstract: The Ebola virus, a member of the Filoviridae family, causes severe hemorrhagic fever in humans. Filamentous virions contain a helical nucleocapsid responsible for genome transcription, replication, ...The Ebola virus, a member of the Filoviridae family, causes severe hemorrhagic fever in humans. Filamentous virions contain a helical nucleocapsid responsible for genome transcription, replication, and packaging into progeny virions. The nucleocapsid consists of a helical nucleoprotein (NP)-viral genomic RNA complex forming the core structure, to which VP24 and VP35 bind externally. Two NPs, each paired with a VP24 molecule, constitute a repeating unit. However, the detailed nucleocapsid structure remains unclear. Here, we determine the nucleocapsid-like structure within virus-like particles at 4.6 Å resolution using single-particle cryo-electron microscopy. Mutational analysis identifies specific interactions between the two NPs and two VP24s and demonstrates that each of the two VP24s in different orientations distinctively regulates nucleocapsid assembly, viral RNA synthesis, intracellular transport of the nucleocapsid, and infectious virion production. Our findings highlight the sophisticated mechanisms underlying the assembly and functional regulation of the nucleocapsid and provide insights into antiviral development.
History
DepositionFeb 6, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39081.png

Downloads & links

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Map

FileDownload / File: emd_39081.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 256 pix.
= 316.8 Å		1.24 Å/pix.
x 256 pix.
= 316.8 Å		1.24 Å/pix.
x 256 pix.
= 316.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.46236306 - 0.7614814
Average (Standard dev.)0.0013070235 (±0.022102227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39081_msk_1.map
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Additional map: #1

Fileemd_39081_additional_1.map
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Half map: #2

Fileemd_39081_half_map_1.map
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Half map: #1

Fileemd_39081_half_map_2.map
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Sample components

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Entire : Zaire ebolavirus

EntireName: Zaire ebolavirus
Components
  • Virus: Zaire ebolavirus
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Membrane-associated protein VP24
    • RNA: RNA (12-MER)

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Supramolecule #1: Zaire ebolavirus

SupramoleculeName: Zaire ebolavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 186538 / Sci species name: Zaire ebolavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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: 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
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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Macromolecule #3: RNA (12-MER)

MacromoleculeName: RNA (12-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Molecular weightTheoretical: 3.629032 KDa
SequenceString:
UUUUUUUUUU UU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMTris-HCltris hydroxymethyl aminomethane hydrochloride
150.0 mMNaClsodium chloride
1.0 mMEDTAethylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
Details: The sample was applied to both sides of the grid. The grids were blotted for 14 seconds..
DetailsThe total 2.5 microlitre sample was applied to both sides of the glow-discharged grid.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH)
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5897 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 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

Particle selectionNumber selected: 263789
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ehm


Details: 5Z9W and 4M0Q were also used to make an initial model, fitted into 6EHM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 204348
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6ehm

source_name: PDB, initial_model_type: experimental model

5z9w

source_name: PDB, initial_model_type: experimental model

4m0q

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8y9j:
Structure of the Ebola virus nucleocapsid subunit

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