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

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Entry
Database: PDB / ID: 2wfs
TitleFitting of influenza virus NP structure into the 9-fold symmetryzed cryoEM reconstruction of an active RNP particle.
DescriptorNUCLEOPROTEIN
KeywordsVIRAL PROTEIN / VIRAL NUCLEOPROTEIN / HOST-VIRUS INTERACTION / RNA VIRUSES / NUCLEOPROTEIN / RIBONUCLEOPROTEIN / RNA / VIRION / NUCLEUS / INFLUENZA / RNA-BINDING
Specimen sourceINFLUENZA A VIRUS / virus
MethodElectron microscopy (12 Å resolution / Particle / Single particle)
AuthorsColoma, R. / Valpuesta, J.M. / Arranz, R. / Carrascosa, J.L. / Ortin, J. / Martin-Benito, J.
CitationPLoS Pathog., 2009, 5, e1000491-e1000491

PLoS Pathog., 2009, 5, e1000491-e1000491 StrPapers
The structure of a biologically active influenza virus ribonucleoprotein complex.
Rocío Coloma / José M Valpuesta / Rocío Arranz / José L Carrascosa / Juan Ortín / Jaime Martín-Benito

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 15, 2009 / Release: Jul 7, 2009
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 7, 2009Structure modelrepositoryInitial release
1.1Dec 28, 2011Structure modelDatabase references / Version format compliance
1.2Aug 30, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id

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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
Polyers511,2549
Non-polymers00
Water0
#1
A: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#2
B: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#3
C: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#4
D: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#5
E: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#6
F: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#7
G: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#8
H: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#9
I: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8061
Polyers56,8061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)
NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N


Mass: 56806.047 Da / Num. of mol.: 9 / Source: (gene. exp.) INFLUENZA A VIRUS / virus

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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
Details: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE
pH: 8
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

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

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1SitusMODEL FITTING1
2SPIDERRECONSTRUCTION1
CTF correctionDetails: WHOLE PLATE
SymmetryPoint symmetry: C9
3D reconstructionMethod: ANGULAR RECONSTITUTION,ITERATIVE ALGEBRAIC RECONSTRUCTION
Resolution: 12 Å / Number of particles: 9571 / Actual pixel size: 2.8
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1603.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RIGID BODY / Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL / Target criteria: VOLUMETRIC
Atomic model buildingPDB-ID: 2IQH
Least-squares processHighest resolution: 12 Å
Refine hist #LASTHighest resolution: 12 Å
Number of atoms included #LASTProtein: 15336 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 15336

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