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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
DescriptorELONGATION FACTOR 3A
KeywordsNUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / PHOSPHORYLATION / ELONGATION FACTOR / RNA-BINDING / ATP-BINDING / RRNA-BINDING
Specimen sourceSaccharomyces cerevisiae / yeast / BAKER'S YEAST / サッカロミセス・セレビシエ /
MethodElectron microscopy (6 A resolution / Single particle / Vitreous ice (cryo EM))
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. / Kinzy, T.G. / Andersen, G.R. / Beckmann, R.
CitationNature, 2006, 443, 663-668

Nature, 2006, 443, 663-668 StrPapers
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
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

DateDeposition: Jul 7, 2006 / Release: Jul 10, 2007 / Last modification: Apr 14, 2010

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Assembly

Deposited unit
A: ELONGATION FACTOR 3A


Theoretical massNumber of molelcules
Total (without water)109,4421
Polyers109,4421
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

#1: Polypeptide(L)ELONGATION FACTOR 3A / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION FACTOR 3 / EEF3 / YEAST ELONGATION FACTOR 3


Mass: 109442.336 Da / Num. of mol.: 1
Details: TRANSLATION ELONGATION IN FUNGI ABC-TYPE ATPASE TRNA RELEASE
Fragment: RESIDUES 1-976
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P16521

Cellular component

Molecular function

Biological process

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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: 80S-RNC-EEF3-AMP-PNP COMPLEX / Aggregation state: PARTICLE
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
Sample preparationpH: 7.5 / Sample conc.: 0.17 mg/ml
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F30 / Date: Feb 11, 2005
Electron gunAccelerating voltage: 300 kV / Illumination mode: LOW DOSE
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 deg.
CameraType: KODAK SO-163 FILM
EM image scansNumber digital images: 141
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: SPIDER
EM single particle entitySymmetry type: ASYMMETRIC
Least-squares processHighest resolution: 6 A
Refine hist #LASTHighest resolution: 6 A
Number of atoms included #LASTProtein: 7599 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7599

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