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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 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Jun 12, 2003 / Release: Jul 15, 2003 / Last modification: Feb 2, 2010
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)48,1173
Polyers48,1173
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chainP-tRNA


Mass: 20017.092 Da / Num. of mol.: 1
#2: Polypeptide(L)30S ribosomal protein S12


Mass: 13804.441 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


Mass: 14295.032 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenAggregation state: PARTICLE
Component
IDNameAssembly idGo idIpr id
1P-tRNA1
230S ribosomal protein S1210006412006032
350S ribosomal protein L1110006412000911
Sample preparationpH: 7.5 / Sample conc.: 32 mg/ml
Specimen supportDetails: Quantifoil holley-carbon film grids
VitrificationDetails: Rapid-freezing in liquid ethane
Crystal grow
*PLUS
Temp unit: K / Method: electron microscopy / Details: electron microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jun 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2000 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4 nm / Nominal defocus min: 15 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO163 FILM

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Processing

EM single particle entitySymmetry type: ASYMMETRIC
3D reconstructionMethod: 3D projection matching; conjugate gradients with regularization
Resolution: 10.8 A / Actual pixel size: 2.82 A/pix / Magnification calibration: TMV
CTF correction method: CTF correction of 3D-maps by Wiener filtration
Details: SPIDER package. Crystal Structure of Thermus Thermophilus 70S ribosome
Atomic model buildingMethod: Manual fitting in O / Ref space: REAL
Atomic model buildingPDB-ID: 1GIX, 1GIY
Number of atoms included #LASTProtein: 257 / Nucleic acid: 62 / Ligand: 0 / Solvent: 0 / Total: 319

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