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- EMDB-16426: CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid... -

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Basic information

Entry
Database: EMDB / ID: EMD-16426
TitleCryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly multimer
Map dataHendra henipavirus nucleoprotein sauronoid EM density postprocessed map
Sample
  • Complex: Sauronoid assembly of Hendra henipavirus nucleoprotein
    • Protein or peptide: Nucleocapsid
    • RNA: RNA (84-MER)
KeywordsNucleoprotein / RNA-binding protein / Sauronoid / VIRAL PROTEIN
Function / homologyParamyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleocapsid
Function and homology information
Biological speciesHendra henipavirus / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.485 Å
AuthorsPasschier TC / Maskell DP / Edwards TA / Barr JN
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission721367European Union
CitationJournal: Sci Rep / Year: 2024
Title: The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures.
Authors: Tim C Passchier / Joshua B R White / Daniel P Maskell / Matthew J Byrne / Neil A Ranson / Thomas A Edwards / John N Barr /
Abstract: We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound ...We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent N and N protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the N N-terminus and N C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions.
History
DepositionJan 4, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16426.png

Downloads & links

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Map

FileDownload / File: emd_16426.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHendra henipavirus nucleoprotein sauronoid EM density postprocessed map
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.031
Minimum - Maximum-0.05054455 - 0.12061005
Average (Standard dev.)0.0007801891 (±0.0058279606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16426_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Hendra henipavirus nucleoprotein sauronoid EM density half map 2

Fileemd_16426_half_map_1.map
AnnotationHendra henipavirus nucleoprotein sauronoid EM density half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Hendra henipavirus nucleoprotein sauronoid EM density half map 1

Fileemd_16426_half_map_2.map
AnnotationHendra henipavirus nucleoprotein sauronoid EM density half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sauronoid assembly of Hendra henipavirus nucleoprotein

EntireName: Sauronoid assembly of Hendra henipavirus nucleoprotein
Components
  • Complex: Sauronoid assembly of Hendra henipavirus nucleoprotein
    • Protein or peptide: Nucleocapsid
    • RNA: RNA (84-MER)

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Supramolecule #1: Sauronoid assembly of Hendra henipavirus nucleoprotein

SupramoleculeName: Sauronoid assembly of Hendra henipavirus nucleoprotein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed Hendra henipavirus nucleoprotein forming sauronoid complexes.
Source (natural)Organism: Hendra henipavirus
Molecular weightTheoretical: 1.691779 MDa

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Macromolecule #1: Nucleocapsid

MacromoleculeName: Nucleocapsid / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Hendra henipavirus
Molecular weightTheoretical: 58.54132 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDIFDEAAS FRSYQSKLGR DGRASAATAT LTTKIRIFVP ATNSPELRWE LTLFALDVIR SPSAAESMKI GAAFTLISMY SERPGALIR SLLNDPDIEA VIIDVGSMLN GIPVMERRGD KAQEEMEGLM RILKTARESS KGKTPFVDSR AYGLRITDMS T LVSAVITI ...String:
MSDIFDEAAS FRSYQSKLGR DGRASAATAT LTTKIRIFVP ATNSPELRWE LTLFALDVIR SPSAAESMKI GAAFTLISMY SERPGALIR SLLNDPDIEA VIIDVGSMLN GIPVMERRGD KAQEEMEGLM RILKTARESS KGKTPFVDSR AYGLRITDMS T LVSAVITI EAQIWILIAK AVTAPDTAEE SETRRWAKYV QQKRVNPFFA LTQQWLTEMR NLLSQSLSVR KFMVEILMEV KK GGSAKGR AVEIISDIGN YVEETGMAGF FATIRFGLET RYPALALNEF QSDLNTIKGL MLLYREIGPR APYMVLLEES IQT KFAPGG YPLLWSFAMG VATTIDRSMG ALNINRGYLE PMYFRLGQKS ARHHAGGIDQ NMANKLGLNS DQVAELAAAV QETS VGRQD NNMQAREAKF AAGGVLVGGG EQDIDEEEEP IEHSGRQSVT FKREMSMSSL ADSVPSSSVS TSGGTRLTNS LLNLR SRLA AKAIKESTAQ SSSERNPPNN RPQADSGRKD DQEPKPAQND LDFVRADV

UniProtKB: Nucleocapsid

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Macromolecule #2: RNA (84-MER)

MacromoleculeName: RNA (84-MER) / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta 2
Molecular weightTheoretical: 25.672984 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUU

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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

BufferpH: 7.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3548 / Average exposure time: 1.5 sec. / Average electron dose: 59.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 75000
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

Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D14 (2x14 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.485 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5683
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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