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- EMDB-9793: The Cryo-EM structure of nucleoprotein-RNA complex of Newcastle d... -

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Basic information

Entry
Database: EMDB / ID: EMD-9793
TitleThe Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virus
Map data
Sample
  • Complex: Ternary complex of nucleoprotein-RNA of Newcastle disease virus
    • Protein or peptide: Nucleocapsid
    • RNA: polyU
Keywordsself-capping helical structure complex / NUCLEAR PROTEIN / NUCLEAR PROTEIN-RNA complex
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 speciesNewcastle disease virus / Avian avulavirus 1 / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsSong X / Shan H
CitationJournal: Elife / Year: 2019
Title: Self-capping of nucleoprotein filaments protects the Newcastle disease virus genome.
Authors: Xiyong Song / Hong Shan / Yanping Zhu / Shunlin Hu / Ling Xue / Yong Chen / Wei Ding / Tongxin Niu / Jian Gu / Songying Ouyang / Qing-Tao Shen / Zhi-Jie Liu /
Abstract: Non-segmented negative-strand RNA viruses, such as measles, ebola and Newcastle disease viruses (NDV), encapsidate viral genomic RNAs into helical nucleocapsids, which serve as the template for viral ...Non-segmented negative-strand RNA viruses, such as measles, ebola and Newcastle disease viruses (NDV), encapsidate viral genomic RNAs into helical nucleocapsids, which serve as the template for viral replication and transcription. Here, the clam-shaped nucleocapsid structure, where the NDV viral genome is sequestered, was determined at 4.8 Å resolution by cryo-electron microscopy. The clam-shaped structure is composed of two single-turn spirals packed in a back-to-back mode. This tightly packed structure functions as a seed for the assembly of a nucleocapsid from both directions, facilitating the growth of double-headed filaments with two separate RNA strings inside. Disruption of this structure by mutations in its loop interface yielded a single-headed unfunctional filament.
History
DepositionJan 28, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0254
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0254
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jc3
  • Surface level: 0.0254
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jc3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9793.png

Downloads & links

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Map

FileDownload / File: emd_9793.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 290 pix.
= 391.5 Å		1.35 Å/pix.
x 290 pix.
= 391.5 Å		1.35 Å/pix.
x 290 pix.
= 391.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0254 / Movie #1: 0.0254
Minimum - Maximum-0.044319578 - 0.095486015
Average (Standard dev.)0.0008160225 (±0.0058264495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 391.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z391.500391.500391.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290290
D min/max/mean-0.0440.0950.001

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Supplemental data

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Sample components

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Entire : Ternary complex of nucleoprotein-RNA of Newcastle disease virus

EntireName: Ternary complex of nucleoprotein-RNA of Newcastle disease virus
Components
  • Complex: Ternary complex of nucleoprotein-RNA of Newcastle disease virus
    • Protein or peptide: Nucleocapsid
    • RNA: polyU

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Supramolecule #1: Ternary complex of nucleoprotein-RNA of Newcastle disease virus

SupramoleculeName: Ternary complex of nucleoprotein-RNA of Newcastle disease virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Newcastle disease virus

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Macromolecule #1: Nucleocapsid

MacromoleculeName: Nucleocapsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Avian avulavirus 1
Molecular weightTheoretical: 43.830703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSVFDEYEQ LLAAQTRPNG ALGGGEKGST LKVEVPVFTL NSDDPEDRWN FAVFCLRIAV SEDANKPLRQ GALISLLCSH SQVMRNHVA LAGKQNEATL AVLEIDGFTN GVPQFNNRSG VSEERAQRFM MIAGSLPRAC SNGTPFVTAG VEDDAPEDIT D TLERILSI ...String:
MSSVFDEYEQ LLAAQTRPNG ALGGGEKGST LKVEVPVFTL NSDDPEDRWN FAVFCLRIAV SEDANKPLRQ GALISLLCSH SQVMRNHVA LAGKQNEATL AVLEIDGFTN GVPQFNNRSG VSEERAQRFM MIAGSLPRAC SNGTPFVTAG VEDDAPEDIT D TLERILSI QAQVWVTVAK AMTAYETADE SETRRINKYM QQGRVQKKYI LHPVCRSAIQ LTIRQSLAVR IFLVSELKRG RN TAGGTST YYNLVGDVDS YIRNTGLTAF FLTLKYGINT KTSALALSSL SGDIQKMKQL MRLYRMKGDN APYMTLLGDS DQM SFAPAE YAQLYSFAMG MASVLDKGTG KYQFARDFMS TSFWRLGVEY AQAQGSSINE DMAAELKLTP AARRGLAAAA QR

UniProtKB: Nucleocapsid

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Macromolecule #2: polyU

MacromoleculeName: polyU / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

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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: 8
GridPretreatment - Type: GLOW DISCHARGE / Details: GLOW DISCHARGED
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 75290
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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