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- PDB-2ob7: Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM -

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Database: PDB / ID: 2ob7
TitleStructure of tmRNA-(SmpB)2 complex as inferred from cryo-EM
DescriptorSsrA-binding protein/RNA Complex
Specimen sourceThermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
MethodElectron microscopy (13.6 Å resolution / Particle / Single particle)
AuthorsFrank, J. / Felden, B. / Gillet, R. / Li, W.
CitationJ. Biol. Chem., 2007, 282, 6356-6363

primary. J. Biol. Chem., 2007, 282, 6356-6363 Yorodumi Papers
Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Reynald Gillet / Sukhjit Kaur / Wen Li / Marc Hallier / Brice Felden / Joachim Frank

#1. Proc.Natl.Acad.Sci.USA, 2006, 103, 16484-16489
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome
Kaur, S. / Gillet, R. / Li, W. / Gursky, R. / Frank, J.

#2. Science, 2003, 300, 127-130
Visualizing tmRNA entry into a stalled ribosome
Valle, M. / Gillet, R. / Kaur, K. / Henne, A. / Ramakrishnan, V. / Frank, J.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 18, 2006 / Release: Jan 23, 2007
RevisionDateData content typeGroupProviderType
1.0Jan 23, 2007Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE The deposited entry is a model to fit the cryo-EM map of tmRNA+SmpB(2) from Thermus thermophilus. The deposition includes 4 chains: chain A: tmRNA model chains B,C: SmpB (from 1P6V.pdb chain A, for SmpB from AQUIFEX AEOLICUS); chain D: helix 44 of 30S ribosomal subunit (from 1N34.pdb chain A:1406-1496. X-ray structure of 1N34 is from Thermus thermophilus). The E.coli model eschcolitm3D-model-72.pdb (http://www.ag.auburn.edu/mirror/tmRDB/rna/tmrna.html/) was used as a template to build the model by replacing several fragments which have x-ray crystal as alternatives, and by fitting all the structures into the cryo-EM maps. Nucleotide numbering in this model follows E.coli sequence. Considering the differences between tmRNA sequences from E.coli and T.thermophilus, a small number of nucleotides in the template model are not included in this model.

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Deposited unit
A: transfer-messenger RNA
D: 16S ribosomal RNA
B: SsrA-binding protein
C: SsrA-binding protein

Theoretical massNumber of molelcules
Total (without water)170,5984

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: RNA chaintransfer-messenger RNA / Coordinate model: P atoms only

Mass: 105728.523 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
#2: RNA chain16S ribosomal RNA / Coordinate model: P atoms only

Mass: 27987.715 Da / Num. of mol.: 1 / Details: helix 44 of 30S ribosomal subunit
Source: (natural) Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
#3: Polypeptide(L)SsrA-binding protein / Coordinate model: Cα atoms only

Mass: 18440.818 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス

Cellular component

Molecular function

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Pre-accommodated ribosomal trans-translation complex: T. thermophilus 70S-mRNA-(P-site tRNA)-tmRNA-(SmpB)2-(EF-Tu)-GDP-kirromycin
Details: see Experimental Procedures in Kaur et al. (PNAS). [Deposition refers to structure of tmRNA-(SmpB)2 complex derived by fitting of EM map from Kaur et al. Fitting was modified in Gillet et al.]
Buffer solutionName: polimix / Details: polimix / pH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: This grid plus sample was kept at -80 degree C for several days before use.
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: Blot for 5 seconds before plunging. Rapid plunge freezing in liquid ethane.

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jun 1, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 55000 / Calibrated magnification: 49000 / Nominal defocus max: 3635 nm / Nominal defocus min: 1475 nm / Cs: 2 mm
Specimen holderTemperature: 296 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM


EM software
CTF correctionDetails: CTF correction of each defocus group reconstruction, by Wiener filtering
SymmetryPoint symmetry: C1
3D reconstructionMethod: single particle reconstruction / Resolution: 13.6 Å / Number of particles: 52829 / Nominal pixel size: 2.82 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--manual fitting using stereo visualization REFINEMENT PROTOCOL--Manual
Ref protocol: OTHER / Ref space: REAL
Atomic model buildingPDB-ID: 1P6V
Number of atoms included #LASTProtein: 237 / Nucleic acid: 414 / Ligand: 0 / Solvent: 0 / Total: 651

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