3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1327

Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 22.408501399, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 22.408501399, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1327
TitleReconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
MapReconstruction of the 43S preinitiation complex from S. cerevisiae.
SampleEukaryotic translation preinitiation complex 43S
AuthorsGilbert RJC, Gordiyenko Y, von der Haar T, Sonnen AF-P, Hoffman GW, Nardelli M, Stuart DI, McCarthy JEG
DateDeposition: 2007-03-06, Header release: 2007-03-06, Map release: 2007-04-06, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 22.408501399, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 22.408501399, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres
List of similar structure data Omokage searchabout Omokage system
Article
Citation - Primary
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
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
Keywords5' Untranslated Regions, Codon, Initiator, Cryoelectron Microscopy, Eukaryotic Initiation Factor-1 (genetics), Eukaryotic Initiation Factor-2 (genetics), Eukaryotic Initiation Factor-3 (genetics), Eukaryotic Initiation Factor-5 (genetics), Models, Chemical, Models, Molecular, Protein Binding, Protein Biosynthesis, Protein Structure, Secondary, Protein Subunits, RNA, Fungal (genetics), RNA, Messenger (metabolism), Ribosomes (chemistry), Saccharomyces cerevisiae (genetics)
LinksDOI: 10.1073/pnas.0606880104, PubMed: 17389391, PMC: PMC1832216
Map
Fileemd_1327.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesY (Sec.)X (Row.)Z (Col.)
128 pix
3.33 A/pix
= 426.24 A
128 pix
3.33 A/pix
= 426.24 A
128 pix
3.33 A/pix
= 426.24 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:21.7, 22.4085014 (movie #1):
Minimum - Maximum: -97.4 - 200
Average (Standard dev.): 1.93102 (13.2256)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderZXY
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
Unit CellA= B= C: 426.24 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.33 A
CCP4 map header info
modeImage stored as Reals
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/S312
start NC/NR/NS-64-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-97.400200.0001.931
Annotation DetailsReconstruction of the 43S preinitiation complex from S. cerevisiae.
Supplement
Images
Images
Sample
NameEukaryotic translation preinitiation complex 43S
Oligomeric State40S-Met-tRNA-eIF2-GMP-PNP-eIF3-eIF1-eIF1A
Number of Components6
Theoretical Mass1.941MDa
Component #1: ribosome-eukaryote - 40S
Scientific nameSmall subunit
Common Name40S
Theoretical Mass1.4 MDa
Experimental Mass1.4 MDa
DetailsS. cerevisiae
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
EukaryoteSSU 40S
Recombinant expressionNo
Component #2: nucleic-acid - tRNA
Scientific nametRNA
Theoretical Mass0.023 MDa
Experimental Mass0.023 MDa
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
SyntheticNo
StructureDOUBLE HELIX
ClassT-RNA
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
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell Location: Cytosol
Engineered SourceNCBI taxonomy: 4932
Expression system: Saccharomyces 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
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell Location: Cytosol
Engineered SourceNCBI taxonomy: 4932
Expression system: Saccharomyces 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
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell Location: Cytosol
Engineered SourceNCBI taxonomy: 4932
Expression system: Saccharomyces 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
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell Location: Cytosol
Engineered SourceNCBI taxonomy: 4932
Expression system: Saccharomyces cerevisiae
Experiment
Sample Preparation
Specimen Support Details300 mesh copper grid with lacey carbon film
Specimen Stateparticle
BufferDetails: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP
pH: 7.4
Vitrification
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
MethodBlot with Whatman number 1 paper for 1-2 seconds prior to plunging.
DetailsVitrification instrument: Home-made plunger
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
AstigmatismAstigmatism corrected at 100,000 x
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2055 nm - 11685 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature100 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images70
Sampling Size8.33
Quant Bit Number8
ScannerOTHER
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmSingle particle
SoftwareIMAGIC, EMAN, FREALIGN, SPIDER, GAP
CTF CorrectionPer micrograph
Resolution By Author20 A
Resolution MethodFSC 0.5
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.
Single Particle
Number of Projections27101
DetailsThe particles were selected manually.
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
Target CriteriaReal space CC and R-factor
SoftwareGAP
Refinement SpaceREAL
DetailsProtocol: Rigid body
Download
Data from EMDB
Header (meta data in XML format)emd-1327.xml (12.5 KB)
Map dataemd_1327.map.gz (342.4 KB)
Images1327.gif (53.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1327
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 19.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 19.9 KB