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- EMDB-12584: CryoEM structure of the Nipah virus nucleocapsid spiral clam-shap... -

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Basic information

Entry
Database: EMDB / ID: EMD-12584
TitleCryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly
Map data
Sample
  • Complex: Nipah virus nucleocapsid Protein-RNA complex
    • Complex: Nucleoprotein
      • Protein or peptide: Nucleoprotein
    • Complex: RNA (48-MER)
      • RNA: RNA (48-MER)
    • Complex: RNA (42-MER)
      • RNA: RNA (42-MER)
KeywordsProtein-RNA complex / Nucleocapsid / VIRAL PROTEIN
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / host cell cytoplasm / molecular adaptor activity / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesNipah virus / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKer DS / Jenkins HT
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: PLoS Pathog / Year: 2021
Title: CryoEM structure of the Nipah virus nucleocapsid assembly.
Authors: De-Sheng Ker / Huw T Jenkins / Sandra J Greive / Alfred A Antson /
Abstract: Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we ...Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the "3-bases-in, 3-bases-out" conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123-139, which may serve as a valuable epitope for surveillance and diagnostics.
History
DepositionMar 9, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nt6
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7nt6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12584.png

Downloads & links

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Map

FileDownload / File: emd_12584.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 200 pix.
= 314.4 Å		1.57 Å/pix.
x 200 pix.
= 314.4 Å		1.57 Å/pix.
x 200 pix.
= 314.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.572 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.04259262 - 0.09261534
Average (Standard dev.)0.0014660218 (±0.0059324396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 314.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5721.5721.572
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z314.400314.400314.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0430.0930.001

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Supplemental data

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Mask #1

Fileemd_12584_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12584_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12584_half_map_2.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 : Nipah virus nucleocapsid Protein-RNA complex

EntireName: Nipah virus nucleocapsid Protein-RNA complex
Components
  • Complex: Nipah virus nucleocapsid Protein-RNA complex
    • Complex: Nucleoprotein
      • Protein or peptide: Nucleoprotein
    • Complex: RNA (48-MER)
      • RNA: RNA (48-MER)
    • Complex: RNA (42-MER)
      • RNA: RNA (42-MER)

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Supramolecule #1: Nipah virus nucleocapsid Protein-RNA complex

SupramoleculeName: Nipah virus nucleocapsid Protein-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1 MDa

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Supramolecule #2: Nucleoprotein

SupramoleculeName: Nucleoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Nipah virus

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Supramolecule #3: RNA (48-MER)

SupramoleculeName: RNA (48-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #4: RNA (42-MER)

SupramoleculeName: RNA (42-MER) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Nipah virus
Molecular weightTheoretical: 60.609484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLEVLFQG PAMSDIFEEA ASFRSYQSKL GRDGRASAAT ATLTTKIRIF VPATNSPELR WELTLFALDV IRSPSAAES MKVGAAFTLI SMYSERPGAL IRSLLNDPDI EAVIIDVGSM VNGIPVMERR GDKAQEEMEG LMRILKTARD S SKGKTPFV ...String:
MGSSHHHHHH SSGLEVLFQG PAMSDIFEEA ASFRSYQSKL GRDGRASAAT ATLTTKIRIF VPATNSPELR WELTLFALDV IRSPSAAES MKVGAAFTLI SMYSERPGAL IRSLLNDPDI EAVIIDVGSM VNGIPVMERR GDKAQEEMEG LMRILKTARD S SKGKTPFV DSRAYGLRIT DMSTLVSAVI TIEAQIWILI AKAVTAPDTA EESETRRWAK YVQQKRVNPF FALTQQWLTE MR NLLSQSL SVRKFMVEIL IEVKKGGSAK GRAVEIISDI GNYVEETGMA GFFATIRFGL ETRYPALALN EFQSDLNTIK SLM LLYREI GPRAPYMVLL EESIQTKFAP GGYPLLWSFA MGVATTIDRS MGALNINRGY LEPMYFRLGQ KSARHHAGGI DQNM ANRLG LSSDQVAELA AAVQETSAGR QESNVQAREA KFAAGGVLIG GSDQDIDEGE EPIEQSGRQS VTFKREMSIS SLANS VPSS SVSTSGGTRL TNSLLNLRSR LAAKAAKEAA SSNATDDPAI SNRTQGESEK KNNQDLKPAQ NDLDFVRADV

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (48-MER)

MacromoleculeName: RNA (48-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 14.650994 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUU

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Macromolecule #3: RNA (42-MER)

MacromoleculeName: RNA (42-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 12.814002 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU 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

Concentration0.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
300.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.5 µm
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: 217522
Startup modelType of model: EMDB MAP
EMDB ID:

0141


Details: The map is cropped to represent a single turn and low pass filtered to 60 angstorm
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 23029
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1beta)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7nt5


Chain - Chain ID: H / Chain - Residue range: 4-397 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7nt6:
CryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly

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