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MODEL FOR EEF3 BOUND TO AN 80S RIBOSOME

by single particle reconstruction, at 9.9 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1233, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1233, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
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.
DateDeposition: 2006-07-07, Release: 2007-07-10
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Sequence detailsPDB LACKS THE C-TERMINAL PART OF EEF3 (RESIDUES 977-1044)
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1233, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1233, Image by UCSF CHIMERA

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EMDB-1233

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Article
Citation - primary
ArticleNature, Vol. 443, Issue 7112, Page 663-8, Year 2006
TitleStructure of eEF3 and the mechanism of transfer RNA release from the E-site.
AuthorsChristian 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
Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark.
KeywordsAdenosine Diphosphate (chemistry), Adenosine Triphosphate (analogs & derivatives), Binding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Fungal Proteins (chemistry), Gene Expression Regulation, Fungal, Models, Biological, Models, Molecular, Peptide Elongation Factors (chemistry), Protein Conformation, RNA, Transfer (metabolism, 9014-25-9), Ribosomes (chemistry), Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins, Structure-Activity Relationship, YEF3 protein, S cerevisiae
LinksDOI: 10.1038/nature05126, PubMed: 16929303
Components
ID 1 : EF-3A, EF-3, TRANSLATION ELONGATION FACTOR 3A, EUKARYOTIC ELONGATION FACTOR 3, EEF3, YEAST ELONGATION FACTOR 3
Image
DescriptionELONGATION FACTOR 3A
Typepolypeptide(L)
FragmentRESIDUES 1-976
Formula weight109442.336 Da
Number of molecules1
ID1
DetailsTRANSLATION ELONGATION IN FUNGI ABC-TYPE ATPASE TRNA RELEASE
SourceMethod: Isolated from a genetically manipulated source
Gene: BAKER'S YEAST, ID:4932, SACCHAROMYCES CEREVISIAE
Host: ID:4932, SACCHAROMYCES CEREVISIAE

, WCGA
Plasmid name: PYES2.1-TOPO
LinksUniProt: P16521, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Name80S-RNC-EEF3-AMP-PNP COMPLEX
Buffer
Name20MM 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
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration0.17 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsLIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2005-02-11
Electron gun
Accelerating voltage300 kV
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 38900 X, Nominal: 39000 X
CsNominal: 2.7 mm
Nominal defocusMax: 3500 nm, Min: 1200 nm
Specimen holder
Tilt angleMin: 0 degrees
Temperature95 Kelvin
Detector
TypeKODAK SO-163 FILM
Image scans
Number digital images141
Processing
2D projection selection
Software nameSPIDER
Single particle entity
Symmetry typeASYMMETRIC
Refine
Refine idELECTRON MICROSCOPY
Ls d res high6.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high6.00
Total atoms7599
Protein atoms7599
Download
PDB format
Allpdb2ix8.ent.gz
pdb2ix8.ent (uncompressed file)
Header onlypdb2ix8.ent.gz
mmCIF format
mmCIF2ix8.cif.gz
XML format
All2ix8.xml.gz
No-atom2ix8-noatom.xml.gz
Ext-atom2ix8-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5 MB