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- PDB-2ix8: MODEL FOR EEF3 BOUND TO AN 80S RIBOSOME -

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Basic information

Entry
Database: PDB / ID: 2ix8
TitleMODEL FOR EEF3 BOUND TO AN 80S RIBOSOME
ComponentsELONGATION FACTOR 3A
KeywordsNUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / PHOSPHORYLATION / ELONGATION FACTOR / RNA-BINDING / ATP-BINDING / RRNA-BINDING
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / translational termination / cytosolic ribosome / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / rRNA binding ...translational elongation / translation elongation factor activity / translational termination / cytosolic ribosome / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / rRNA binding / ribosome / ATP hydrolysis activity / ATP binding
Similarity search - Function
Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / HEAT repeat profile. / HEAT, type 2 / ABC transporter-like, conserved site / ABC transporters family signature. ...Four helical bundle domain / : / Four helical bundle domain / Elongation Factor 3 / : / : / HEAT repeat profile. / HEAT, type 2 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Armadillo-like helical / Armadillo-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor 3A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsAndersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. ...Andersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. / Kinzy, T.G. / Andersen, G.R. / Beckmann, R.
CitationJournal: Nature / Year: 2006
Title: Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss ...Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss Kinzy / Gregers R Andersen / Roland Beckmann /
Abstract: Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of ...Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release.
History
DepositionJul 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _refine.ls_d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure viewerMolecule:
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Assembly

Deposited unit
A: ELONGATION FACTOR 3A


Theoretical massNumber of molelcules
Total (without water)109,4421
Polymers109,4421
Non-polymers00
Water00
1


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

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Components

#1: Protein ELONGATION FACTOR 3A / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION FACTOR 3 / EEF3 / YEAST ...EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION FACTOR 3 / EEF3 / YEAST ELONGATION FACTOR 3


Mass: 109441.547 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-976
Source method: isolated from a genetically manipulated source
Details: TRANSLATION ELONGATION IN FUNGI ABC-TYPE ATPASE TRNA RELEASE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PYES2.1-TOPO / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): WCGA / References: UniProt: P16521
Has protein modificationY
Sequence detailsPDB LACKS THE C-TERMINAL PART OF EEF3 (RESIDUES 977-1044)

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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-RNC-EEF3-AMP-PNP COMPLEX / Type: RIBOSOME
Buffer solutionName: 20MM HEPES,PH 7.5,10MM MG(OAC)2,150MM KOAC 1MM DTT,0.05% NIKKOL, 125MM SUCROSE,0.01MG -ML-1 CYCLOHEXIMIDE,0.5MM AMP-PNP,0.1MM NEOMYCIN, 0.3% DESOXYBIGCHAPS
pH: 7.5
Details: 20MM HEPES,PH 7.5,10MM MG(OAC)2,150MM KOAC 1MM DTT,0.05% NIKKOL, 125MM SUCROSE,0.01MG -ML-1 CYCLOHEXIMIDE,0.5MM AMP-PNP,0.1MM NEOMYCIN, 0.3% DESOXYBIGCHAPS
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Feb 11, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38900 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 95 K / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 141
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Omodel fitting
2Situsmodel fitting
3SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37700 / Symmetry type: POINT
RefinementHighest resolution: 9.9 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7599 0 0 0 7599

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