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- PDB-1jqm: Fitting of L11 protein and elongation factor G (EF-G) in the cryo... -

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Entry
Database: PDB / ID: 1jqm
TitleFitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid
Components
  • 50S Ribosomal protein L11
  • Elongation Factor G
KeywordsRIBOSOME / L11 / EF-G / cryo-EM / 70s E.coli ribosome / GDP state
Function / homology
Function and homology information


ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / GTPase activity ...ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / GTPase activity / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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/L12 / Ribosomal protein L11, RNA binding domain / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor G / 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
Model detailsThis structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. ...This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G- (GDP 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. The structure is modeled as a C-alpha trace. Conformational changes occur in protein L11 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. 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.
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.
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,8292
Polymers91,8292
Non-polymers00
Water00
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
#2: Protein Elongation Factor G / EF-G / translation elongation factor EF-G / Coordinate model: Cα atoms only


Mass: 76963.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: EF-G from E. coli 70S ribosome modeled by crystal structure of EF-G from Thermus thermophilus
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P13551

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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 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome map. L11 (linker region between N and C terminal) and EF- ...Text: This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GDP 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, GDP and fusidic acid
Type: RIBOSOME
Buffer solutionpH: 7.6
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 FIELD / 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

Particle selectionNum. of particles selected: 36113
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 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome electron ...Details: 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 (GDP 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 in two steps due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. 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. atoms824 0 0 0 824
NMR software
NameVersionDeveloperClassification
IRIS Explorer3.5Numerical Algorithms Group, Inc.data 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 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. These changed conformations were modeled ...Details: Conformational changes occur in protein L11 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. 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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