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Yorodumi- 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 | ||||||
Components | Elongation factor Tu-B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Transition state / conserved switch I / Antibiotic resistance / Elongation factor / GTP-binding / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis | ||||||
Function / homology | Function and homology information translation elongation factor activity / GTPase activity / GTP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.6 Å | ||||||
Authors | Nissen, P. / Nyborg, J. / Kjeldgaard, M. | ||||||
Citation | Journal: J Mol Biol / Year: 2008 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3dwu.cif.gz | 10.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dwu.ent.gz | 3.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dwu_validation.pdf.gz | 715.7 KB | Display | wwPDB validaton report |
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Full document | 3dwu_full_validation.pdf.gz | 715.2 KB | Display | |
Data in XML | 3dwu_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 3dwu_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/3dwu ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dwu | HTTPS FTP |
-Related structure data
Related structure data | 5015MC 5017MC 5016C 3dnyC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / DSM 579 / References: UniProt: P60339 |
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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 |
-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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
-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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