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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 A resolution / Single particle / Vitreous ice cryo EM)
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

DateDeposition: Apr 15, 2009 / Release: Jul 7, 2009 / Last modification: Dec 28, 2011

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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)511,2599
Polyers511,2599
Non-polymers00
Water0
#1
A: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#2
B: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#3
C: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#4
D: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#5
E: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#6
F: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#7
G: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#8
H: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#9
I: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)56,8071
Polyers56,8071
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: 56806.586 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE CRYO EM

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Sample preparation

Assembly of specimenName: INFLUENZA VIRUS RIBONUCLEOPROTEIN PARTICLE / Aggregation state: PARTICLE
Details: MICROGRAPHS SELECTED BY COMPUTED CTF DATA AQUISITION
Buffer solutionName: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE
Sample preparationpH: 8
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: CRYOGEN - ETHANE INSTRUMENT - LEICA PLUNGER

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI G2
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.26
Specimen holderTemperature: 99
CameraType: FILM (KODAK SO-136)
EM image scansNumber digital images: 159

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Processing

Image selectionSoftware name: SPIDER / Number of particles: 9571
EM single particle entitySymmetry type: MIXED SYMMETRY
3D reconstructionMethod: ANGULAR RECONSTITUTION,ITERATIVE ALGEBRAIC RECONSTRUCTION
Resolution: 12 / Actual pixel size: 2.8 / CTF correction method: WHOLE PLATE
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1603.
Atomic model buildingMethod: RIGID BODY / Ref space: RECIPROCAL / Target criteria: VOLUMETRIC
Atomic model buildingPDB-ID: 2IQH
Least-squares processHighest resolution: 12
Refine hist #LASTHighest resolution: 12
Number of atoms included #LASTProtein: 15336 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 15336

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