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- PDB-4bkk: The Respiratory Syncytial Virus nucleoprotein-RNA complex forms a... -

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Basic information

Entry
Database: PDB / ID: 4bkk
TitleThe Respiratory Syncytial Virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.
Components
  • NUCLEOPROTEIN
  • RNA (161-MER)
KeywordsVIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / PKR-mediated signaling / Evasion by RSV of host interferon responses / viral capsid / symbiont-mediated suppression of host NF-kappaB cascade / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS A STRAIN LONG
MethodELECTRON MICROSCOPY / electron tomography / negative staining
AuthorsBakker, S.E. / Duquerroy, S. / Galloux, M. / Loney, C. / Conner, E. / Eleouet, J.F. / Rey, F.A. / Bhella, D.
CitationJournal: J Gen Virol / Year: 2013
Title: The respiratory syncytial virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.
Authors: Saskia E Bakker / Stéphane Duquerroy / Marie Galloux / Colin Loney / Edward Conner / Jean-François Eléouët / Félix A Rey / David Bhella /
Abstract: Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical ...Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC helix would be right-handed, as the N-N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a left-handed helix. We further show that the contacts in the ring can be distorted to maintain key N-N-protein interactions in a left-handed helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.
History
DepositionApr 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / em_software ...diffrn_radiation_wavelength / em_software / entity / entity_src_gen
Item: _em_software.image_processing_id / _em_software.name / _entity.src_method
Revision 1.2Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA (161-MER)
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN
M: NUCLEOPROTEIN
N: NUCLEOPROTEIN
O: NUCLEOPROTEIN
P: NUCLEOPROTEIN
Q: NUCLEOPROTEIN
R: NUCLEOPROTEIN
S: NUCLEOPROTEIN
T: NUCLEOPROTEIN
U: NUCLEOPROTEIN
V: NUCLEOPROTEIN
W: NUCLEOPROTEIN
X: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)1,049,77024
Polymers1,049,77024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

#1: RNA chain RNA (161-MER)


Mass: 49089.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A STRAIN LONG
Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
#2: Protein ...
NUCLEOPROTEIN / PROTEIN N / NUCLEOCAPSID PROTEIN


Mass: 43507.848 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A STRAIN LONG
Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P03418

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: PURIFIED RECOMBINANT RSV NUCLEOCAPSIDS. / Type: VIRUS
Buffer solutionName: 50 MM TRIS-HCL, PH 7.4, 150 MM NACL, 10 MM EDTA / pH: 7.4 / Details: 50 MM TRIS-HCL, PH 7.4, 150 MM NACL, 10 MM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Ammonium Molybdate
Specimen supportDetails: HOLEY CARBON

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Electron microscopy imaging

MicroscopyModel: JEOL 2200FSC / Date: Jul 15, 2010
Details: ROOM TEMPERATURE STAINED GRIDS IMAGED AT LN2 TEMPERATURES.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTilt angle max: 60 ° / Tilt angle min: -60 °
Image recordingElectron dose: 131 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 9
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Dynamo3D reconstruction
2eTomo3D reconstruction
3D reconstructionMethod: SUBTOMOGRAM AVERAGING / Num. of particles: 911 / Nominal pixel size: 6.5 Å
Details: SUBTOMOGRAM AVERAGING. NOTE THE COORDINATES ARE BASED ON MODELLING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2369. (DEPOSITION ID: 11640).
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Details: METHOD--MODELLING REFINEMENT PROTOCOL--MODEL
Atomic model buildingPDB-ID: 2WJ8

2wj8


Accession code: 2WJ8 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms66263 3220 0 0 69483

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