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- EMDB-12582: CryoEM structure of Nipah virus nucleocapsid semi-spiral clam-sha... -

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Basic information

Entry
Database: EMDB / ID: EMD-12582
TitleCryoEM structure of Nipah virus nucleocapsid semi-spiral clam-shaped assembly
Map data
Sample
  • Complex: Nipah virus nucleocapsid Protein-RNA complex
    • Protein or peptide: Nucleocapsid 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 henipavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsKer DS / Jenkins HT / Greive SJ / Antson AA
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-
UpdateAug 4, 2021-
Current statusAug 4, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12582.png

Downloads & links

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Map

FileDownload / File: emd_12582.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.572 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.034075353 - 0.081518576
Average (Standard dev.)0.0011349272 (±0.0069079576)
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
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0340.0820.001

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Supplemental data

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Mask #1

Fileemd_12582_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12582_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12582_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
    • Protein or peptide: Nucleocapsid protein

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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
Source (natural)Organism: Nipah henipavirus
Recombinant expressionOrganism: Escherichia coli bl (bacteria)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Nucleocapsid protein

MacromoleculeName: Nucleocapsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Nipah henipavirus
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLEVLFQG PAMSDIFEEA ASFRSYQSKL GRDGRASAAT ATLTTKIRI FVPATNSPEL RWELTLFALD VIRSPSAAES MKVGAAFTLI S MYSERPGA LIRSLLNDPD IEAVIIDVGS MVNGIPVMER RGDKAQEEME GL MRILKTA RDSSKGKTPF ...String:
MGSSHHHHHH SSGLEVLFQG PAMSDIFEEA ASFRSYQSKL GRDGRASAAT ATLTTKIRI FVPATNSPEL RWELTLFALD VIRSPSAAES MKVGAAFTLI S MYSERPGA LIRSLLNDPD IEAVIIDVGS MVNGIPVMER RGDKAQEEME GL MRILKTA RDSSKGKTPF VDSRAYGLRI TDMSTLVSAV ITIEAQIWIL IAK AVTAPD TAEESETRRW AKYVQQKRVN PFFALTQQWL TEMRNLLSQS LSVR KFMVE ILIEVKKGGS AKGRAVEIIS DIGNYVEETG MAGFFATIRF GLETR YPAL ALNEFQSDLN TIKSLMLLYR EIGPRAPYMV LLEESIQTKF APGGYP LLW SFAMGVATTI DRSMGALNIN RGYLEPMYFR LGQKSARHHA GGIDQNM AN RLGLSSDQVA ELAAAVQETS AGRQESNVQA REAKFAAGGV LIGGSDQD I DEGEEPIEQS GRQSVTFKRE MSISSLANSV PSSSVSTSGG TRLTNSLLN LRSRLAAKAA KEAASSNATD DPAISNRTQG ESEKKNNQDL KPAQNDLDFV RADV

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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 / 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
CTF correctionSoftware - Name: CTFFIND (ver. 4)
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 angstrom
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 18979
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1beta)
FSC plot (resolution estimation)

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