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- PDB-2p8z: Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDPNP:sordarin... -

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Basic information

Entry
Database: PDB / ID: 2p8z
TitleFitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDPNP:sordarin cryo-EM reconstruction
Components
  • Elongation factor 2EEF2
  • Elongation factor Tu-B
KeywordsTRANSLATION / elongation / translocation / GTPase / 80S ribosome
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / protein-folding chaperone binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / 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 / 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
ADENOSINE-5-DIPHOSPHORIBOSE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-SO1 / Elongation factor 2 / Elongation factor Tu-B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Thermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsTaylor, D.J. / Nilsson, J. / Merrill, A.R. / Andersen, G.R. / Nissen, P. / Frank, J.
CitationJournal: EMBO J / Year: 2007
Title: Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
Authors: Derek J Taylor / Jakob Nilsson / A Rod Merrill / Gregers Rom Andersen / Poul Nissen / Joachim Frank /
Abstract: On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 ...On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit.
History
DepositionMar 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Database references / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / struct_conn / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

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Assembly

Deposited unit
T: Elongation factor 2
S: Elongation factor Tu-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9555
Polymers97,3782
Non-polymers1,5763
Water0
1


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

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Components

#1: Protein Elongation factor 2 / EEF2 / EF-2 / Translation elongation factor 2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase


Mass: 93549.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324
#2: Protein/peptide Elongation factor Tu-B / EF-Tu-B


Mass: 3829.122 Da / Num. of mol.: 1 / Fragment: SWITCH 1 LOOP / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60339
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical ChemComp-SO1 / [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID / SORDARIN


Mass: 494.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42O8
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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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: 80S ribosomeEukaryotic ribosome / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenConc.: 0.096 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey-Carbon film grids
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: rapid-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jul 7, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Calibrated magnification: 37642 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1400 nm / Cs: 2.26 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1RSRefmodel fittingTNT implementation of RSRef
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D-maps by Wiener filtration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D projection matching, conjugate gradients with regularization
Resolution: 8.9 Å / Num. of particles: 102689 / Nominal pixel size: 1.86 Å / Actual pixel size: 1.86 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingB value: 15 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Maximization of correlation-coefficient
Details: METHOD--Real-space refinement using rigid bodies REFINEMENT PROTOCOL--TNT implementation of RSRef
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
11U2RT1
21EFTS1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 102 0 6713

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