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- PDB-3dwu: Transition-state model conformation of the switch I region fitted... -
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Basic information
Entry | Database: PDB / ID: 3dwu | ||||||
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Title | Transition-state model conformation of the switch I region fitted into the cryo-EM map of the eEF2.80S.AlF4.GDP complex | ||||||
![]() | Elongation factor Tu-B | ||||||
![]() | BIOSYNTHETIC PROTEIN / Transition state / conserved switch I / Antibiotic resistance / Elongation factor / GTP-binding / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis | ||||||
Function / homology | ![]() translation elongation factor activity / GTPase activity / GTP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.6 Å | ||||||
![]() | Nissen, P. / Nyborg, J. / Kjeldgaard, M. | ||||||
![]() | ![]() Title: Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy. Authors: Jayati Sengupta / Jakob Nilsson / Richard Gursky / Morten Kjeldgaard / Poul Nissen / Joachim Frank / ![]() Abstract: In an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum ...In an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum tetrafluoride and GDP, with aluminum tetrafluoride mimicking the gamma-phosphate during hydrolysis. This is the first visualization of a structure representing a transition-state complex on the ribosome. Tight interactions are observed between the factor's G domain and the large ribosomal subunit, as well as between domain IV and an intersubunit bridge. In contrast, some of the domains of eEF2 implicated in small subunit binding display a large degree of flexibility. Furthermore, we find support for a transition-state model conformation of the switch I region in this complex where the reoriented switch I region interacts with a conserved rRNA region of the 40S subunit formed by loops of the 18S RNA helices 8 and 14. This complex is structurally distinct from the eEF2-bound 80S ribosome complexes previously reported, and analysis of this map sheds light on the GTPase-coupled translocation mechanism. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 10.7 KB | Display | ![]() |
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PDB format | ![]() | 3.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 715.7 KB | Display | ![]() |
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Full document | ![]() | 715.2 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5015MC ![]() 5017MC ![]() 5016C ![]() 3dnyC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein/peptide | Mass: 4949.441 Da / Num. of mol.: 1 / Fragment: Switch I region: UNP residues 21-66 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: eEF2.80S.AlF4.GDP complex / Type: RIBOSOME |
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Buffer solution | Name: 20 mM Hepes-NH3, 100 mM KCl, 20 mM MgCl2 / pH: 7.2 / Details: 20 mM Hepes-NH3, 100 mM KCl, 20 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: NITROGEN Details: Cryogen ETHANE (93K), two-face blotting for 1 second |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49650 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 10 e/Å2 / Details: Kodak SO163 film |
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Processing
EM software |
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CTF correction | Details: segregation in defocus groups and correction in volumes | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: SPIDER / Resolution: 12.6 Å / Resolution method: FSC / Num. of particles: 28242 / Nominal pixel size: 2.82 Å Details: Single particle reconstruction, resolution estimated: FSC cut-off at 0.15 Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient Details: METHOD--manual REFINEMENT PROTOCOL--Fitted as rigid body. Current model was aligned to the helix A of the fitted eEF2 coordinates (PDB entry 3DNY) which is located next to the switch I ...Details: METHOD--manual REFINEMENT PROTOCOL--Fitted as rigid body. Current model was aligned to the helix A of the fitted eEF2 coordinates (PDB entry 3DNY) which is located next to the switch I sequence. The coordinates for this entry are based on manual fitting of the coordinates into cryo-EM density map. Therefore, authors did not deposit structure factors. | ||||||||||||
Atomic model building | PDB-ID: 3DNY Accession code: 3DNY / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST /
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