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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
TitleTransition-state model conformation of the switch I region fitted into the cryo-EM map of the eEF2.80S.AlF4.GDP complex
ComponentsElongation factor Tu-B
KeywordsBIOSYNTHETIC 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 / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor Tu-B
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.6 Å
AuthorsNissen, P. / Nyborg, J. / Kjeldgaard, M.
CitationJournal: 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
DepositionJul 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Elongation factor Tu-B


Theoretical massNumber of molelcules
Total (without water)4,9491
Polymers4,9491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Elongation factor Tu-B / EF-Tu-B / Coordinate model: Cα atoms only


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: eEF2.80S.AlF4.GDP complex / Type: RIBOSOME
Buffer solutionName: 20 mM Hepes-NH3, 100 mM KCl, 20 mM MgCl2 / pH: 7.2 / Details: 20 mM Hepes-NH3, 100 mM KCl, 20 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: 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
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 49650 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 10 e/Å2 / Details: Kodak SO163 film

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Processing

EM software
IDNameCategory
1Omodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: segregation in defocus groups and correction in volumes
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 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 buildingProtocol: 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 buildingPDB-ID: 3DNY

3dny


Accession code: 3DNY / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST /
ProteinNucleic acidLigandSolventTotal
Num. atoms46 0 0 0 46

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