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- PDB-1jqs: Fitting of L11 protein and elongation factor G (domain G' and V) ... -
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Basic information
Entry | Database: PDB / ID: 1jqs | ||||||
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Title | Fitting 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 | ||||||
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![]() | RIBOSOME / L11 / EF-G / cryo-EM / 70S E.coli ribosome / GTP state | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Molecular Modeling based on crystal structures / cryo EM / Resolution: 18 Å | ||||||
![]() | Agrawal, R.K. / Linde, J. / Segupta, J. / Nierhaus, K.H. / Frank, J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
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PDBx/mmCIF format | ![]() | 19.6 KB | Display | ![]() |
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PDB format | ![]() | 8.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 279.2 KB | Display | ![]() |
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Full document | ![]() | 278.8 KB | Display | |
Data in XML | ![]() | 704 B | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | 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) ![]() ![]() |
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#2: Protein/peptide | Mass: 3599.001 Da / Num. of mol.: 1 / Fragment: part of domain G' / 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) ![]() ![]() |
#3: Protein | Mass: 7637.778 Da / Num. of mol.: 1 / Fragment: domain V / 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) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
NMR details | Text: 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- ...Text: 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
Component | Name: E. coli 70S ribosome bound with EF-G and GMPPCP / Type: RIBOSOME |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Crystal grow | *PLUS Method: electron microscopy |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS EM420 |
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Electron gun | Electron source: OTHER / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 52000 X |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: GENERIC FILM |
Image scans | Scanner model: PERKIN ELMER |
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Processing
Particle selection | Num. of particles selected: 36113 | ||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 36113 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: 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 (GTP 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 (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. | ||||||||||||||||||||
Refinement step | Cycle: LAST
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NMR software |
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Refinement | Method: 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 ...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. |