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- PDB-1pn7: Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray s... -

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Basic information

Entry
Database: PDB / ID: 1pn7
TitleCoordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome
DescriptorRNA BINDING PROTEIN/RNA Complex
KeywordsRNA binding protein/RNA / ribosomal protein / tRNA binding protein / tRNA / RNA binding protein-RNA COMPLEX
Specimen sourceThermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
Thermotoga maritima / bacteria / thermophilic / サーモトガ・マリティマ
MethodElectron microscopy (10.8 Å resolution / Particle / Single particle)
AuthorsValle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J.
CitationCell, 2003, 114, 123-134

Cell, 2003, 114, 123-134 StrPapers
Locking and unlocking of ribosomal motions.
Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 12, 2003 / Release: Jul 15, 2003
RevisionDateData content typeGroupProviderType
1.0Jul 15, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999The structure contains C alpha atoms only

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Assembly

Deposited unit
C: P-tRNA
O: 30S ribosomal protein S12
L: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)48,1163
Polyers48,1163
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chainP-tRNA / Coordinate model: P atoms only


Mass: 20016.959 Da / Num. of mol.: 1
#2: Polypeptide(L)30S ribosomal protein S12 / Coordinate model: Cα atoms only


Mass: 13804.311 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus / bacteria / thermophilic / サームス・サーモフィラス
References: UniProt: Q5SHN3

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)50S ribosomal protein L11 / Coordinate model: Cα atoms only


Mass: 14294.913 Da / Num. of mol.: 1
Source: (natural) Thermotoga maritima / bacteria / thermophilic / サーモトガ・マリティマ
References: UniProt: P29395

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
1E.coli 70S ribosomeRIBOSOME0
2P-tRNA1
330S ribosomal protein S121
450S ribosomal protein L111
Buffer solutionpH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holley-carbon film grids
VitrificationCryogen name: ETHANE / Details: Rapid-freezing in liquid ethane
Crystal grow
*PLUS
Temp unit: K / Method: electron microscopy / Details: electron microscopy

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jun 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 49696 / Nominal defocus max: 4 nm / Nominal defocus min: 15 nm / Cs: 2 mm
Specimen holderTemperature: 93 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: CTF correction of 3D-maps by Wiener filtration
SymmetryPoint symmetry: C1
3D reconstructionMethod: 3D projection matching; conjugate gradients with regularization
Resolution: 10.8 Å / Actual pixel size: 2.82 / Magnification calibration: TMV
Details: SPIDER package. Crystal Structure of Thermus Thermophilus 70S ribosome
Symmetry type: POINT
Atomic model buildingDetails: METHOD--Manual fitting in O / Ref protocol: OTHER / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11GIX1
21GIY1
Number of atoms included #LASTProtein: 257 / Nucleic acid: 62 / Ligand: 0 / Solvent: 0 / Total: 319

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