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

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Basic information

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 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 21, 2007 / Release: Jan 15, 2008
RevisionDateData content typeGroupProviderType
1.0Jan 15, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Mar 12, 2014Structure modelDerived calculations

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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)404,60214
Polyers404,60214
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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Fragment of 16S rRNA ... , 3 types, 3 molecules ABC

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


Mass: 3827.336 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#2: RNA chainFragment of 16S rRNA (h15)


Mass: 9048.452 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#3: RNA chainFragment of 16S rRNA (h44)


Mass: 31208.635 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 118505352

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RNA chain , 2 types, 2 molecules DM

#4: RNA chain16S ribosomal RNA (H5)


Mass: 98292.133 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 48256
#10: RNA chainp/E-tRNA


Mass: 23728.123 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus

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Fragment of23S rRNA ... , 5 types, 5 molecules FGHIJ

#5: RNA chainFragment of23S rRNA (H95)


Mass: 9378.643 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#6: RNA chainFragment of23S rRNA (H68)


Mass: 17631.637 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 37223182
#7: RNA chainFragment of23S rRNA (H89)


Mass: 13540.067 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus
#8: RNA chainFragment of23S rRNA (H42-44)


Mass: 18710.129 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 37223182
#9: RNA chainFragment of23S rRNA (H76)


Mass: 33148.680 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: GenBank: 37223182

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

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


Mass: 14920.754 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: 29317.703 Da / Num. of mol.: 1 / Source: (natural) Thermus thermophilus / References: UniProt: P80371

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 2 molecules KL

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


Mass: 24872.721 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: 76977.102 Da / Num. of mol.: 1 / Source: (gene. exp.) Thermus thermophilus / References: UniProt: P13551

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

Component
IDNameTypeParent ID
1complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNPRIBOSOME0
230S ribosomal protein S121
350S ribosomal protein L11
4Elongation factor G1
530S ribosomal protein S21
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
Details: 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
pH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder type: Eucentric
Image recordingElectron dose: 19 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

SoftwareName: SPIDER / Classification: refinement
EM software
IDNameCategory
1SitusMODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: defocus groups
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.3 Å / Number of particles: 77038
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.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--Rigid Body / Ref protocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting ID
12J001
21GIX1
32J011
41FNM1
51YL31
Number of atoms included #LASTProtein: 9140 / Nucleic acid: 9891 / Ligand: 0 / Solvent: 0 / Total: 19031

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