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- PDB-1jqs: Fitting of L11 protein and elongation factor G (domain G' and V) ... -

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Entry
Database: PDB / ID: 1jqs
TitleFitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog
Components
  • (Elongation Factor GEF-G) x 2
  • 50S Ribosomal protein L11
KeywordsRIBOSOME / L11 / EF-G / cryo-EM / 70S E.coli ribosome / GTP state
Function / homologyTranslation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold / Small GTP-binding protein domain / Translation elongation factor EFG/EF2, domain IV / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, RNA binding domain / Elongation factor G, domain III / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L11, C-terminal / Translation elongation factor EFTu-like, domain 2 ...Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold / Small GTP-binding protein domain / Translation elongation factor EFG/EF2, domain IV / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, RNA binding domain / Elongation factor G, domain III / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L11, C-terminal / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / P-loop containing nucleoside triphosphate hydrolase / Tr-type G domain, conserved site / EF-G domain III/V-like / EFG, domain V / Ribosomal protein L11, C-terminal domain superfamily / Translation elongation factor EFG/EF2 / Ribosomal protein L11/L12 / Elongation factor Tu GTP binding domain / Transcription factor, GTP-binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L11 signature. / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L11, N-terminal domain / Elongation factor G, domain IV / Ribosomal protein L11/L12, N-terminal domain superfamily / Elongation factor Tu domain 2 / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / GTPase activity, coupled / translational elongation / translation elongation factor activity / large ribosomal subunit rRNA binding / GDP binding / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / intracellular / rRNA binding / structural constituent of ribosome / translation / GTP binding / magnesium ion binding / cytoplasm / Elongation factor G / 50S ribosomal protein L11
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / Molecular Modeling based on crystal structures / cryo EM / 18 Å resolution
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: Embo J. / Year: 1994
Title: The Crystal Structure of Elongation Factor G Complexed with GDP, at 2.7A Resolution.
Authors: Czworkowski, J. / Wang, J. / Steitz, T.A. / Moore, P.B.
#3: Journal: Embo J. / Year: 1994
Title: Three-dimensional structure of the ribosomal translocase: Elongation factor G from Thermus thermophilus
Authors: AEvarsson, A. / Brazhnikov, E. / Garber, M. / Zheltonosova, J. / Chirgadze, Y. / al-Karadaghi, S. / Svensson, L.A. / Liljas, A.
#4: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of a Mutant EF-G Reveals Domain III and Possibly the Fusidic Acid Binding Site
Authors: Laurberg, M. / Kristensen, O. / Martemyanov, K. / Gudkov, A.T. / Nagaev, I. / Hughes, D. / Liljas, A.
#5: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 7, 2001 / Release: Sep 7, 2001
RevisionDateData content typeGroupProviderType
1.0Sep 7, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: 50S Ribosomal protein L11
B: Elongation Factor G
C: Elongation Factor G


Theoretical massNumber of molelcules
Total (without water)26,1023
Polyers26,1023
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 14865.637 Da / Num. of mol.: 1
Details: L11 from E. coli 70S ribosome modeled by crystal structure of L11 from Thermatogoma maritima
Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P29395
#2: Protein/peptide Elongation Factor G / EF-G / EF-G / translation elongation factor EF-G / Coordinate model: Cα atoms only


Mass: 3599.001 Da / Num. of mol.: 1
Details: EF-G from E. coli 70S ribosome modeled by crystal structure of EF-G from Thermus thermophilus
Fragment: part of domain G' / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P13551
#3: Protein/peptide Elongation Factor G / EF-G / EF-G / translation elongation factor EF-G / Coordinate model: Cα atoms only


Mass: 7637.778 Da / Num. of mol.: 1
Details: EF-G from E. coli 70S ribosome modeled by crystal structure of EF-G from Thermus thermophilus
Fragment: domain V / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P13551

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction
NMR detailsText: This structure was generated by fitting the X-ray crystal structures of L11 and EF-G into the 70S E. coli EF-G (GTP form) bound ribosome map. L11(linker region between N and C terminal) and EF-G positions of domains G' and V were modeled to accommodate the conformational changes.

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Sample preparation

ComponentName: E. coli 70S ribosome bound with EF-G and GMPPCP / 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

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

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Processing

Particle selectionNumber of particles selected: 36113
SymmetryPoint symmetry: C1
3D reconstructionResolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 36113 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GTP form) bound ribosome electron microscopy map. L11 (linker region between N and C terminal) and EF-G positions of domains G and V were modeled to accommodate the conformational changes. 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.
Ref protocol: OTHER / Ref space: REAL / Target criteria: VISUAL AGREEMENT
Number of atoms included #LASTProtein: 233 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 233
NMR software
NameVersionDeveloperClassification
IRIS Explorer3.5Numerical Algorithms Group, Incdata analysis
O5.10Jones, 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 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.

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