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- PDB-2wfs: Fitting of influenza virus NP structure into the 9-fold symmetryz... -

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Basic information

Entry
Database: PDB / ID: 2wfs
TitleFitting of influenza virus NP structure into the 9-fold symmetryzed cryoEM reconstruction of an active RNP particle.
ComponentsNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / VIRAL NUCLEOPROTEIN / HOST-VIRUS INTERACTION / RNA VIRUSES / NUCLEOPROTEIN / RIBONUCLEOPROTEIN / RNA / VIRION / NUCLEUS / INFLUENZA / RNA-BINDING
Function / homology
Function and homology information


cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / helical viral capsid / Viral mRNA Translation / viral penetration into host nucleus / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesINFLUENZA A VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsColoma, R. / Valpuesta, J.M. / Arranz, R. / Carrascosa, J.L. / Ortin, J. / Martin-Benito, J.
CitationJournal: PLoS Pathog / Year: 2009
Title: The structure of a biologically active influenza virus ribonucleoprotein complex.
Authors: Rocío Coloma / José M Valpuesta / Rocío Arranz / José L Carrascosa / Juan Ortín / Jaime Martín-Benito /
Abstract: The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein ...The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein particles (RNPs), which are responsible for virus transcription and replication. Despite their importance, information about the structure of these RNPs is scarce. We have determined the three-dimensional structure of a biologically active recombinant RNP by cryo-electron microscopy. The structure shows a nonameric nucleoprotein ring (at 12 Angstrom resolution) with two monomers connected to the polymerase complex (at 18 Angstrom resolution). Docking the atomic structures of the nucleoprotein and polymerase domains, as well as mutational analyses, has allowed us to define the interactions between the functional elements of the RNP and to propose the location of the viral RNA. Our results provide the first model for a functional negative-stranded RNA virus ribonucleoprotein complex. The structure reported here will serve as a framework to generate a quasi-atomic model of the molecular machine responsible for viral RNA synthesis and to test new models for virus RNA replication and transcription.
History
DepositionApr 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Version format compliance
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
E: NUCLEOPROTEIN
F: NUCLEOPROTEIN
G: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)511,2549
Polymers511,2549
Non-polymers00
Water0
1
A: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polymers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
NUCLEOPROTEIN / / NUCLEOCAPSID PROTEIN / PROTEIN N


Mass: 56806.047 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/75 (H3N2) / Gene: NP / Organ (production host): KIDNEY / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: P03466*PLUS

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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: INFLUENZA VIRUS RIBONUCLEOPROTEIN PARTICLE / Type: VIRUS
Details: MICROGRAPHS SELECTED BY COMPUTED CTF DATA AQUISITION
Buffer solutionName: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE
pH: 8
Details: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Details: CRYOGEN - ETHANE INSTRUMENT - LEICA PLUNGER

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm
Specimen holderTemperature: 99 K
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 159

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: WHOLE PLATE
SymmetryPoint symmetry: C9 (9 fold cyclic)
3D reconstructionMethod: ANGULAR RECONSTITUTION,ITERATIVE ALGEBRAIC RECONSTRUCTION
Resolution: 12 Å / Num. of particles: 9571 / Actual pixel size: 2.8 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1603.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: VOLUMETRIC / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 2IQH
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15336 0 0 0 15336

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