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- PDB-4uft: Structure of the helical Measles virus nucleocapsid -

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Basic information

Entry
Database: PDB / ID: 4uft
TitleStructure of the helical Measles virus nucleocapsid
Components
  • 5'-R(*CP*CP*CP*CP*CP*CP)-3'
  • NUCLEOPROTEIN
KeywordsRNA BINDING PROTEIN / MEASLES VIRUS NUCLEOCAPSID / TRANSCRIPTION AND REPLICATION TEMPLATE
Function / homology
Function and homology information


helical viral capsid / viral process / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesMEASLES VIRUS STRAIN HALLE
SPODOPTERA FRUGIPERDA (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsGutsche, I. / Desfosses, A. / Effantin, G. / Ling, W.L. / Haupt, M. / Ruigrok, R.W.H. / Sachse, C. / Schoehn, G.
CitationJournal: Science / Year: 2015
Title: Structural virology. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid.
Authors: Irina Gutsche / Ambroise Desfosses / Grégory Effantin / Wai Li Ling / Melina Haupt / Rob W H Ruigrok / Carsten Sachse / Guy Schoehn /
Abstract: Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the ...Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an RNA at a resolution of 4.3 angstroms. The resulting pseudoatomic model of the measles virus nucleocapsid offers important insights into the mechanism of the helical polymerization of nucleocapsids of negative-strand RNA viruses, in particular via the exchange subdomains of the nucleoprotein. The structure reveals the mode of the nucleoprotein-RNA interaction and explains why each nucleoprotein of measles virus binds six nucleotides, whereas the respiratory syncytial virus nucleoprotein binds seven. It provides a rational basis for further analysis of measles virus replication and transcription, and reveals potential targets for drug design.
History
DepositionMar 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Derived calculations / Other
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_image_scans / em_imaging / em_software
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min ..._em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-2867
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2867
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-2867
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NUCLEOPROTEIN
R: 5'-R(*CP*CP*CP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)45,2932
Polymers45,2932
Non-polymers00
Water0
1
B: NUCLEOPROTEIN
R: 5'-R(*CP*CP*CP*CP*CP*CP)-3'
x 39


Theoretical massNumber of molelcules
Total (without water)1,766,41778
Polymers1,766,41778
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation39
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 39 / Rise per n subunits: 4.015 Å / Rotation per n subunits: -29.173 °)

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Components

#1: Protein NUCLEOPROTEIN /


Mass: 43506.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NUCLEOPROTEIN WAS PARTIALLY DIGESTED WITH TRYPSIN / Source: (gene. exp.) MEASLES VIRUS STRAIN HALLE / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P10050
#2: RNA chain 5'-R(*CP*CP*CP*CP*CP*CP)-3'


Mass: 1786.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPODOPTERA FRUGIPERDA (fall armyworm)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RECOMBINANT MEASLES NUCLEOPROTEIN-RNA HELICAL ASSEMBLY (NUCLEOCAPSID)
Type: COMPLEX
Buffer solutionName: IN 20 MM TRIHCL PH 7.5, 150 MM NACL / pH: 7.5 / Details: IN 20 MM TRIHCL PH 7.5, 150 MM NACL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jul 1, 2013
Details: SPECIAL CARE WAS TAKEN TO PERFORM A COMA-FREE ALIGNMENT OF THE MICROSCOPE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2MODELLERmodel fitting
3PHENIXmodel fitting
4UCSF Chimeramodel fitting
5SPRING3D reconstruction
CTF correctionDetails: EACH PARTICLE
3D reconstructionMethod: WEIGHTED BACK-PROJECTION / Resolution: 4.3 Å / Num. of particles: 228165 / Nominal pixel size: 1.186 Å / Actual pixel size: 1.186 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2867. (DEPOSITION ID: 13046).
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2WJ8

2wj8

RefinementHighest resolution: 4.3 Å
Refinement stepCycle: LAST / Highest resolution: 4.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 120 0 0 3073

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