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- PDB-1zn1: Coordinates of RRF fitted into Cryo-EM map of the 70S post-termin... -

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Entry
Database: PDB / ID: 1zn1
TitleCoordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex
DescriptorRibosome recycling factor/30S ribosomal protein S12/RNA Complex
KeywordsBIOSYNTHETIC/structural protein/RNA / ribosome recycling factor / elongation factor G / 70S / post-termination complex / BIOSYNTHETIC-structural protein-RNA COMPLEX
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (14.1 Å resolution / Particle / Single particle)
AuthorsGao, N. / Zavialov, A.V. / Li, W. / Sengupta, J. / Valle, M. / Gursky, R.P. / Ehrenberg, M. / Frank, J.
CitationMol. Cell, 2005, 18, 663-674

primary. Mol. Cell, 2005, 18, 663-674 StrPapers
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank

#1. Cell(Cambridge,Mass.), 2003, 114, 123-134
Locking and unlocking of ribosomal motions
Valle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J.

#2. Cell(Cambridge,Mass.), 2003, 113, 789-801
Study of structural dynamics of E.coli 70S ribosome using real-space refinement
Gao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Roey, Pl Van / Agrawal, R.K. / Harvey, S.C. / Sali, A. / Chapman, M.S. / Frank, J.

#3. Embo J., 2000, 19, 2362-2370
Crystal structure of the ribosome recycling factor from E.coli
Kim, K.K. / Min, K. / Suh, S.W.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 11, 2005 / Release: Jun 14, 2005
RevisionDateData content typeGroupProviderType
1.0Jun 14, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE This entry contains C alpha and P atoms only.

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Assembly

Deposited unit
B: ribosomal 23S RNA
C: ribosomal 16S RNA
A: Ribosome recycling factor
L: 30S ribosomal protein S12


Theoretical massNumber of molelcules
Total (without water)63,4414
Polyers63,4414
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chainribosomal 23S RNA / Coordinate model: P atoms only


Mass: 18952.248 Da / Num. of mol.: 1 / Fragment: fragment of large subunit rRNA helix 69-71
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
#2: RNA chainribosomal 16S RNA / Coordinate model: P atoms only


Mass: 12988.728 Da / Num. of mol.: 1 / Fragment: fragment of small subunit rRNA helix 44
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
#3: Polypeptide(L)Ribosome recycling factor / Ribosome releasing factor / RRF / Coordinate model: Cα atoms only


Mass: 20671.621 Da / Num. of mol.: 1
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0A805

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S12 / Coordinate model: Cα atoms only


Mass: 10828.608 Da / Num. of mol.: 1
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P0A7S3

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

ComponentName: 70S ribosome / Type: RIBOSOME
Buffer solutionName: Polymix buffer / Details: Polymix buffer / pH: 7.5
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey carbon film grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Feb 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 49700 / Nominal defocus max: -3.8 nm / Nominal defocus min: -1.4 nm
Specimen holderTemperature: 93 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

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Processing

CTF correctionDetails: CTF correction of 3D maps by Wiener filtration
SymmetryPoint symmetry: C1
3D reconstructionMethod: 3D projection matching; conjugate gradient with regularization
Resolution: 14.1 Å / Number of particles: 37379 / Actual pixel size: 2.82 / Magnification calibration: TMV / Details: SPIDER package / 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
11P6G1
21P851
31EK81
Number of atoms included #LASTProtein: 282 / Nucleic acid: 99 / Ligand: 0 / Solvent: 0 / Total: 381

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