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- PDB-3eq3: Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state ... -

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Basic information

Entry
Database: PDB / ID: 3eq3
TitleModel of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM
DescriptorElongation factor Tu
30S ribosomal protein S12
50S ribosomal protein L11/RNA complex
KeywordsRIBOSOMAL PROTEIN/RNA / protein translation / ternary complex / A/T-tRNA / automated data collection / Antibiotic resistance / Elongation factor / GTP-binding / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / RIBOSOMAL PROTEIN-RNA COMPLEX
Specimen sourceEscherichia coli k12 / bacteria / image: Escherichia coli
MethodElectron microscopy (9 A resolution)
AuthorsFrank, J. / Li, W. / Agirrezabala, X.
CitationEMBO J., 2008, 27, 3322-3331

EMBO J., 2008, 27, 3322-3331 StrPapers
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
Wen Li / Xabier Agirrezabala / Jianlin Lei / Lamine Bouakaz / Julie L Brunelle / Rodrigo F Ortiz-Meoz / Rachel Green / Suparna Sanyal / Måns Ehrenberg / Joachim Frank

DateDeposition: Sep 30, 2008 / Release: Dec 16, 2008 / Last modification: May 30, 2012

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Assembly

Deposited unit
X: Elongation factor Tu
L: 30S ribosomal protein S12
I: 50S ribosomal protein L11
Y: tRNA
A: Fragment h18 of the 16S rRNA
C: Fragment h44 of the 16S rRNA
B: Fragment H43-44 of the 23S rRNA
D: Fragment H95 of the 23S rRNA
E: Fragment H69 of the 23S rRNA


Theoretical massNumber of molelcules
Total (without water)131,9799
Polyers131,9799
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Polypeptide(L) , 3 types, 3 molecules XLI

#1: Polypeptide(L)Elongation factor Tu / EF-Tu / P-43


Mass: 43239.738 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12 / References: UniProt: P0A6N1

Cellular component

Molecular function

Biological process

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


Mass: 13637.070 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12 / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S ribosomal protein L11


Mass: 14763.286 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12 / References: UniProt: P0A7J7

Cellular component

Molecular function

Biological process

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RNA chain , 6 types, 6 molecules YACBDE

#4: RNA chaintRNA


Mass: 23844.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#5: RNA chainFragment h18 of the 16S rRNA


Mass: 2871.787 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#6: RNA chainFragment h44 of the 16S rRNA


Mass: 3601.242 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#7: RNA chainFragment H43-44 of the 23S rRNA


Mass: 15504.381 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#8: RNA chainFragment H95 of the 23S rRNA


Mass: 9089.521 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12
#9: RNA chainFragment H69 of the 23S rRNA


Mass: 5427.324 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli K12

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY

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Sample preparation

Assembly of specimenAggregation state: PARTICLE
Composition: A/T-tRNA(Trp), EF-Tu, L11, S12, fragments h44 and h18 from the 16S rRNA, fragments H43-H44, H69, and H95 from the 23S rRNA

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Electron microscopy imaging

MicroscopyDate: Jan 1, 2007
CameraType: AMT
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: RSRef
3D reconstructionMethod: SINGLE PARTICLE / Resolution: 9 A
Atomic model buildingMethod: See Method in the citation / Software name: RSRef / Ref protocol: auto / Ref space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 2AVY, 2AW4, 1QZA, 1OB2
Number of atoms included #LASTProtein: 657 / Nucleic acid: 187 / Ligand: 0 / Solvent: 0 / Total: 844

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