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Eukaryotic translation preinitiation complex 43S
in 'single particle' state, at 30.0 A resolution
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Entry
Database / IDEM DATA BANK (EMDB) / 1331
Sample Name / Map AnnotationEukaryotic translation preinitiation complex 43S
Reconstruction of subclass III from a 31756 image dataset of the 43S eukaryotic translation initiation complex.
AuthorsGilbert RJ, Gordiyenko Y, von der Haar T, Sonnen AF, Hofmann G, Nardelli M, Stuart DI, McCarthy JE
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Cite: data citing same article

Last Update2007-03-06
Map Release Date2007-04-06
EMDB SitesEMDB @EBI (EU) EMDB @RCSB (USA)
Article
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 14, Page 5788-93, Year 2007
TitleReconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
AuthorsRobert J C Gilbert, Yulya Gordiyenko, Tobias von der Haar, Andreas F-P Sonnen, Gregor Hofmann, Maria Nardelli, David I Stuart, John E G McCarthy
AffiliationDivision of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
Chemicals5' Untranslated Regions, Codon, Initiator, Eukaryotic Initiation Factor-1, Eukaryotic Initiation Factor-2, Eukaryotic Initiation Factor-3, Eukaryotic Initiation Factor-5, Protein Subunits, RNA, Fungal, RNA, Messenger
Keywords5' Untranslated Regions, Codon, Initiator, Cryoelectron Microscopy, Eukaryotic Initiation Factor-1, Eukaryotic Initiation Factor-2, Eukaryotic Initiation Factor-3, Eukaryotic Initiation Factor-5, Models, Chemical, Models, Molecular, Protein Binding, Protein Biosynthesis, Protein Structure, Secondary, Protein Subunits, RNA, Fungal, RNA, Messenger, Ribosomes, Saccharomyces cerevisiae
LinksPubMed: 17389391 PubMed Central: 1832216 DOI: 10.1073/pnas.0606880104
Map
Fileemd_1331.map ( map file in CCP4 format, 8389 KB )
ProjectionsProjectionProjectionProjectionProjection
Density
Histogram
Contour Level
(movie #1):		5.9
Minimum: -64.37000
Maximum: 99.60000
Average: 0.79960
Standard dev.: -
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : Y X Z
Dimensions : 128 128 128
Origin : -64 A -64 A -64 A
Limit : 63 A 63 A 63 A
Spacing : 128 A 128 A 128 A
Unit CellA = 426.240 A , B = 426.240 A , C = 426.240 A ,
alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees
Pixel SpacingX = 3.33 A , Y = 3.33 A , Z = 3.33 A
CCP4 map header infounder construction!
mapMAP
mode2
A/pix X/Y/Z3.333.333.33
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z426.240426.240426.240
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S213
start NC/NR/NS-64-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ000
NC,NX/NR,NY/NS,NZ100100100
D min/max/mean-64.37099.6000.800
DetailsCreatedby MAPMAN V.Createdby MAPMAN V. 050302/7.8.1 at Mon Jul 3113:28:09 2006 for gilbert
Created byIMAGIC:CCP4 image = subclass3.map06-03-20 12:21:55
Annotation DetailsReconstruction of subclass III from a 31756 image dataset of the 43S eukaryotic translation initiation complex.
Supplement
Sample
NameEukaryotic translation preinitiation complex 43S
Aggregation State single particle 
Oligomeric State40S-Met-tRNA-eIF2-GMP-PNP-eIF3-eIF1-eIF1A
Number of Components6
Theoretical Mass1.941 MDa
Component #1: ribosome-eukaryote - 40S
Scientific nameSmall subunit
Common Name40S
Theoretical Mass1.4 MDa
Experimental Mass1.4 MDa
DetailsS. cerevisiae
EukaryoteSSU 40S
Component #2: nucleic-acid - tRNA
Scientific nametRNA
Theoretical Mass0.023 MDa
Experimental Mass0.023 MDa
Scientific Name of SpeciesS. cerevisiae
Common Name of Speciesyeast
MutantNo
ClassT-RNA
StructureOTHER
Component #3: protein - eIF2
Scientific nameeukaryotic translation initiation factor 2
Common NameeIF2
Theoretical Mass0.124 MDa
Experimental Mass0.124 MDa
Oligomeric Detailsheterotrimer
Number of Copies1
MutantYes
Natural SourceCell Location: Cytosol
Engineered SourceExp System: S. cerevisiae
Component #4: protein - eIF3
Scientific nameeukaryotic translation initiation factor 3
Common NameeIF3
Theoretical Mass0.362 MDa
Experimental Mass0.362 MDa
Oligomeric DetailsHeteropentamer
Number of Copies1
MutantYes
Natural SourceCell Location: Cytosol
Engineered SourceExp System: S. cerevisiae
Component #5: protein - eIF1
Scientific nameeukaryotic translation initiation factor 1
Common NameeIF1
Theoretical Mass0.012 MDa
Experimental Mass0.012 MDa
Oligomeric DetailsMonomer
Number of Copies1
MutantYes
Natural SourceCell Location: Cytosol
Engineered SourceExp System: S. cerevisiae
Component #6: protein - eIF1A
Scientific nameeukaryotic translation initiation factor 1A
Common NameeIF1A
Theoretical Mass0.017 MDa
Experimental Mass0.017 MDa
Oligomeric DetailsMonomer
Number of Copies1
MutantYes
Natural SourceCell Location: Cytosol
Engineered SourceExp System: S. cerevisiae
Experiment
Sample Preparation
BufferDetails: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP
pH: 7.4
Sample Support Details300 mesh copper grid with lacey carbon film
Vitrification
Cryogen NameETHANE
InstrumentHome-made plunger
MethodBlot with Whatman number 1 paper for 1-2 seconds prior to plunging.
Imaging
MicroscopeFEI/PHILIPS CM200 FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X,
AstigmatismAstigmatism corrected at 100,000 x
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2055 nM - 11685 nM
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Temperature100 Kelvin
Camera
DetectorKodak SO163 film
Image Scans
Number of Digital Images70
Sampling Size8.33 microns
Quant Bit Number8
ScannerOTHER
Processing
3D Reconstruction
AlgorithmSingle particle
SoftwareIMAGIC, EMAN, FREALIGN, SPIDER, GAP
CTF CorrectionPer micrograph
Resolution By Author30.0
Resolution MethodFSC at 0.5 cut-off
Euler Angles DetailsSPIDER Euler angle convention
DetailsFinal maps were computed from CTF-corrected (by phase flipping) images, and scaled in Fourier space to a scattering model of the structure.
EM Data Set ( single particle )
DetailsThe particles were selected manually.
Number of Projections9467
Atomic Model Fitting
Model #0
Refinement ProtocolRigid body
Target CriteriaReal space CC and R-factor
SoftwareGAP
Refinement SpaceREAL
Download
Data from EMDB
Header Informationemd-1331.xml ( XML format, 9,348 byte )
Map Dataemd_1331.map.gz ( 639,213 byte )Details
FTP site (EMDB mirror)EMD-1331
Data from PDBj EM Navigator
movie #1
ASF format (for windows) ( 5,590,831 byte )
MOV format (for Mac) ( 5,568,658 byte )
FLV format (for web page) ( 5,686,927 byte )
Session file for UCSF-Chimera ( 20,083 byte )
movie #2
ASF format (for windows) ( 5,130,031 byte )
MOV format (for Mac) ( 5,154,080 byte )
FLV format (for web page) ( 5,452,846 byte )
Session file for UCSF-Chimera ( 20,381 byte )