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- PDB-2noq: Structure of ribosome-bound cricket paralysis virus IRES RNA -

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Basic information

Entry
Database: PDB / ID: 2noq
TitleStructure of ribosome-bound cricket paralysis virus IRES RNA
DescriptorRibosome
KeywordsRIBOSOME / IRES RNA / Ribosome / Translation / Internal Initiation
Specimen sourceSaccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (7.3 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsSchuler, M. / Connell, S.R. / Lescoute, A. / Giesebrecht, J. / Dabrowski, M. / Schroeer, B. / Mielke, T. / Penczek, P.A. / Westhof, E. / Spahn, C.M.T.
CitationNat. Struct. Mol. Biol., 2006, 13, 1092-1096

Nat. Struct. Mol. Biol., 2006, 13, 1092-1096 StrPapers
Structure of the ribosome-bound cricket paralysis virus IRES RNA.
Martin Schüler / Sean R Connell / Aurelie Lescoute / Jan Giesebrecht / Marylena Dabrowski / Birgit Schroeer / Thorsten Mielke / Pawel A Penczek / Eric Westhof / Christian M T Spahn

DateDeposition: Oct 26, 2006 / Release: Nov 21, 2006 / Last modification: Feb 15, 2012

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Assembly

Deposited unit
A: CrPV IRES
B: 18S ribosomal RNA
C: 18S ribosomal RNA
D: 18S ribosomal RNA
E: 25S ribosomal RNA
F: 40S ribosomal protein S5
G: 60S ribosomal protein L1
H: 60S ribosomal protein L11-B


Theoretical massNumber of molelcules
Total (without water)161,1928
Polyers161,1928
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules AE

#1: RNA chainCrPV IRES


Mass: 60829.207 Da / Num. of mol.: 1 / References: GenBank: 8895506
#5: RNA chain25S ribosomal RNA / S2 / YS8 / RP14


Mass: 17186.404 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae

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18S ribosomal ... , 3 types, 3 molecules BCD

#2: RNA chain18S ribosomal RNA


Mass: 14870.031 Da / Num. of mol.: 1 / Fragment: residues 500-545 / Source: (natural) Saccharomyces cerevisiae
#3: RNA chain18S ribosomal RNA


Mass: 4149.529 Da / Num. of mol.: 1 / Fragment: residues 1050-1062 / Source: (natural) Saccharomyces cerevisiae
#4: RNA chain18S ribosomal RNA


Mass: 4784.906 Da / Num. of mol.: 1 / Fragment: residues 1194-1208 / Source: (natural) Saccharomyces cerevisiae

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Polypeptide(L) , 1 types, 1 molecules F

#6: Polypeptide(L)40S ribosomal protein S5 / L10a


Mass: 16577.305 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P26783

Cellular component

Molecular function

Biological process

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60S ribosomal protein ... , 2 types, 2 molecules GH

#7: Polypeptide(L)60S ribosomal protein L1 / L16 / YL16 / 39B / RP39


Mass: 24014.328 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P53030

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)60S ribosomal protein L11-B


Mass: 18780.684 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q3E757

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: Yeast 80S bound by cricket paralysis virus IRES RNA / Aggregation state: PARTICLE
Buffer solutionName: 20 mM Hepes pH 7.6, 100 mM KAc, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1mM AEBSF, Roche Complete Protease Inhibitor
Specimen supportDetails: Quantifoil

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI-POLARA G2
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300
Electron lensNominal magnification: 39000 / Nominal defocus max: 3900 / Nominal defocus min: 100
CameraType: KODAK SO163 FILM
DetectorType: KODAK SO163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM single particle entitySymmetry type: ASYMMETRIC
3D reconstructionMethod: Iterative 3D-Projection Matching / Resolution: 7.3 / Nominal pixel size: 1.22
Atomic model buildingPDB-ID: 1s1i, 1s1h
Number of atoms included #LASTProtein: 4163 / Nucleic acid: 6746 / Ligand: 0 / Solvent: 0 / Total: 10909

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