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- PDB-1jqt: Fitting of L11 protein in the low resolution cryo-EM map of E.col... -

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Basic information

Entry
Database: PDB / ID: 1jqt
TitleFitting of L11 protein in the low resolution cryo-EM map of E.coli 70S ribosome
Components50S Ribosomal protein L11
KeywordsRIBOSOME / L11 / cryo-EM / 70S E.coli ribosome
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12
Similarity search - Domain/homology
Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / Molecular Modeling based on crystal structures / cryo EM / Resolution: 18 Å
AuthorsAgrawal, R.K. / Linde, J. / Segupta, J. / Nierhaus, K.H. / Frank, J.
Citation
Journal: J Mol Biol / Year: 2001
Title: Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation.
Authors: R K Agrawal / J Linde / J Sengupta / K H Nierhaus / J Frank /
Abstract: L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the ...L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G' domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
Authors: Wimberly, B.T. / Guymon, R. / McCutcheon, J.P. / White, S.W. / Ramakrishnan, V.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: EF-G-dependent GTP hydrolysis induces solution structure of the E. coli 70S ribosome at 11.5A resolution
Authors: Gabashvili, I.S. / Agrawal, R.K. / Spahn, C.M.T. / Grassucci, R.A. / Svergun, D.I. / Frank, J. / Penczek, P.
#3: Journal: Nat.Struct.Biol. / Year: 1999
Title: EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
Authors: Agrawal, R.K. / Heagle, A.B. / Penczek, P. / Grassucci, R.A. / Frank, J.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: 50S Ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)14,8661
Polymers14,8661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 50S Ribosomal protein L11 / / Coordinate model: Cα atoms only


Mass: 14865.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: L11 from E. coli 70S ribosome modeled by crystal structure of L11 from Thermatogoma maritima
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P29395

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
NMR detailsText: This structure was generated by fitting the X-ray crystal structure of L11 into the 70S E. coli ribosome map. L11 (linker region between N and C terminal) was modeled to accommodate the observed densities.

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Sample preparation

ComponentName: 70S ribosomeRibosome / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM420
Electron gunElectron source: OTHER / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 X
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GENERIC FILM

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 36113 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: VISUAL AGREEMENT
Details: REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting the X-ray crystal structure of L11 into the 70S E. coli ribosome map. L11 (linker region between N and C terminal) ...Details: REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting the X-ray crystal structure of L11 into the 70S E. coli ribosome map. L11 (linker region between N and C terminal) was modeled to accommodate the observed densities. Conformational changes occur in protein L11 and EF-G due to the binding of EF-G to the 70S ribosome. These changed conformations were modeled based on the fitting of the crystal coordinates to the low resolution ribosome map (factor-bound) and energy minimizing the fitted structures.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms133 0 0 0 133
NMR software
NameVersionDeveloperClassification
IRIS Explorer3.5Numerical Algorithms Group, Incdata analysis
O5.1Jones, Zou, Cowan, Kjeldgaarddata analysis
SPIDER4.48Frankprocessing
Insight II1998Biosym/MSI Inc.data analysis
RefinementMethod: Molecular Modeling based on crystal structures / Software ordinal: 1
Details: Conformational changes occur in protein L11 when it is bound to 70S ribosome. This changed conformation was modeled based on the fitting of the crystal coordinates to the low resolution ...Details: Conformational changes occur in protein L11 when it is bound to 70S ribosome. This changed conformation was modeled based on the fitting of the crystal coordinates to the low resolution ribosome map and energy minimizing the fitted structures.

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