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- PDB-2om7: Structural Basis for Interaction of the Ribosome with the Switch ... -

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Entry
Database: PDB / ID: 2om7
TitleStructural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors
DescriptorRNA binding protein/RNA Complex
KeywordsRIBOSOME / RNA-Protein Complex
Specimen sourceThermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
MethodElectron microscopy (7.3 A resolution)
AuthorsConnell, S.R. / Wilson, D.N. / Rost, M. / Schueler, M. / Giesebrecht, J. / Dabrowski, M. / Mielke, T. / Fucini, P. / Spahn, C.M.T.
CitationMol. Cell, 2007, 25, 751-764

Mol. Cell, 2007, 25, 751-764 StrPapers
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Sean R Connell / Chie Takemoto / Daniel N Wilson / Hongfei Wang / Kazutaka Murayama / Takaho Terada / Mikako Shirouzu / Maximilian Rost / Martin Schüler / Jan Giesebrecht / Marylena Dabrowski / Thorsten Mielke / Paola Fucini / Shigeyuki Yokoyama / Christian M T Spahn

DateDeposition: Jan 21, 2007 / Release: Jan 15, 2008 / Last modification: Mar 12, 2014

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Assembly

Deposited unit
A: Fragment of 16S rRNA (h14)
B: Fragment of 16S rRNA (h15)
C: Fragment of 16S rRNA (h44)
D: 16S ribosomal RNA (H5)
F: Fragment of23S rRNA (H95)
G: Fragment of23S rRNA (H68)
H: Fragment of23S rRNA (H89)
I: Fragment of23S rRNA (H42-44)
J: Fragment of23S rRNA (H76)
M: p/E-tRNA
E: 30S ribosomal protein S12
K: 50S ribosomal protein L1
L: Elongation factor G
N: 30S ribosomal protein S2


Theoretical massNumber of molelcules
Total (without water)404,60514
Polyers404,60514
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsA model for the entire complex can be generated by aligning the 50s subunit, 30s Head and 30s body from PDB IDs 2j00 and 2j01 to the corresponding elements in this model

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Components

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RNA chain , 10 types, 10 molecules ABCDFGHIJM

#1: RNA chainFragment of 16S rRNA (h14)


Mass: 3827.362 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#2: RNA chainFragment of 16S rRNA (h15)


Mass: 9048.513 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#3: RNA chainFragment of 16S rRNA (h44)


Mass: 31208.826 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 118505352
#4: RNA chain16S ribosomal RNA (H5)


Mass: 98293.047 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 48256
#5: RNA chainFragment of23S rRNA (H95)


Mass: 9378.706 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#6: RNA chainFragment of23S rRNA (H68)


Mass: 17631.746 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 37223182
#7: RNA chainFragment of23S rRNA (H89)


Mass: 13540.153 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#8: RNA chainFragment of23S rRNA (H42-44)


Mass: 18710.258 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 37223182
#9: RNA chainFragment of23S rRNA (H76)


Mass: 33148.875 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 37223182
#10: RNA chainp/E-tRNA


Mass: 23728.281 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus

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30S ribosomal protein ... , 2 types, 2 molecules EN

#11: Polypeptide(L)30S ribosomal protein S12


Mass: 14920.887 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: UniProt: P17293

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S2


Mass: 29317.918 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: UniProt: P80371

Cellular component

Molecular function

Biological process

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50S ribosomal protein ... / Polypeptide(L) , 2 types, 2 molecules KL

#12: Polypeptide(L)50S ribosomal protein L1


Mass: 24872.914 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: UniProt: Q5SLP7

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)Elongation factor G / EF-G


Mass: 76977.914 Da / Num. of mol.: 1 / Source: (gene. exp.) Thermus thermophilus / References: UniProt: P13551

Cellular component

Molecular function

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY

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Sample preparation

Assembly of specimenName: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
Aggregation state: PARTICLE
Component
IDNameAssembly idGo idIpr id
130S ribosomal protein S1210015935005679
250S ribosomal protein L110006412002143
3Elongation factor G10006414004540
430S ribosomal protein S210003735001865
Buffer solutionName: 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
Sample preparationpH: 7.8
VitrificationInstrument: Vitrobot / Cryogen name: ETHANE / Temp: 277 K / Humidity: 95

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 19 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder type: Eucentric
CameraType: 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

SoftwareName: SPIDER / Classification: refinement
Image selectionSoftware name: SPIDER
3D reconstructionResolution: 7.3 A / CTF correction method: defocus groups
Details: The geometry of linkages between some residues in chains J, M and L are distorted. They were not resolved based on the data used for solving this structure.
Atomic model buildingMethod: Rigid Body / Software name: Situs
Atomic model buildingPDB-ID: 2j00, 1gix, 2j01, 1FNM, 1YL3,
Number of atoms included #LASTProtein: 9140 / Nucleic acid: 9891 / Ligand: 0 / Solvent: 0 / Total: 19031

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