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Human 80S ribosome in situ, untreated

by subtomogram averaging, at 39 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.9, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.9, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5224
AuthorsBrandt F, Carlson L-A, Hartl FU, Baumeister W, Grunewald K
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.9, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.9, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleMol. Cell, Vol. 39, Issue 4, Page 560-9, Year 2010
TitleThe three-dimensional organization of polyribosomes in intact human cells.
AuthorsFlorian Brandt, Lars-Anders Carlson, F Ulrich Hartl, Wolfgang Baumeister, Kay Grünewald
Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
KeywordsBinding Sites, Brain Neoplasms (metabolism), Cell Line, Tumor, Electron Microscope Tomography, Glioblastoma (metabolism), Humans, Imaging, Three-Dimensional, Models, Molecular, Polyribosomes (drug effects), Protein Biosynthesis, Protein Conformation, Protein Synthesis Inhibitors (pharmacology), Puromycin (pharmacology, 53-79-2), Structure-Activity Relationship
LinksPII: S1097-2765(10)00613-1, DOI: 10.1016/j.molcel.2010.08.003, PubMed: 20797628
Map
FileEMD-5224.map ( map file in CCP4 format, 444 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.9 (by author), 0.9 (movie #1):
Minimum - Maximum: -2.09170914 - 4.06884241
Average (Standard dev.): 0E-8 (0.99999547)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 48 48 48
Origin : 0 0 0
Limit : 47 47 47
Spacing : 48 48 48
Unit CellA = 394.08002 A , B = 394.08002 A , C = 394.08002 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 8.21 A , Y = 8.21 A , Z = 8.21 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z8.218.218.21
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z394.080394.080394.080
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS484848
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.0924.069-0.000
Annotation DetailsThis is a map of a tomographic average of a human 80S ribosome in situ
Supplement
Sample
NameHuman 80S ribosome in situ, untreated
Number of Components1
Oligomeric StateOne 80S ribosome within mixed cellular polysomes
DetailsCytosolic ribosomes in situ
Mass-estimation MethodSedimentation, 80S
Component #1: ribosome-eukaryote - cytosolic 80S ribosome
Scientific namecytosolic 80S ribosome
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of Specieshuman
EukaryoteALL
Recombinant expressionNo
Experiment
Sample Preparation
StainingCells grown on grids, vitrification
Specimen Stateparticle
Specimen Support DetailsC-flat 2/1, holey carbon gold grid
BufferDetails: Cellular medium, DMEM (Gibco) supplemented with 10% foetal calf serum, 37C and 5% CO2
pH: 7.5
Vitrification
MethodBlot for 2 s before plunging
Cryogen NameETHANE
DetailsVitrification instrument: plunger. Vitrification carried out in air
InstrumentHOMEMADE PLUNGER
Temperature77 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM300FEG/T
Date07-JUL-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose80 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 17500 X, Calibrated: 17500 X
Astigmatismobjective lens astigmatism was corrected at 50,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus5000 nm - 7000 nm
Energy FilterType: GIF2002 , Window: 0-20 eV
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder. ( GATAN LIQUID NITROGEN )
Tilt Angle-65 degrees - 65 degrees
Temperature77 Kelvin ( 77 Kelvin - )
Camera
DetectorGatan 2k x 2k Multiscan CCD camera
Image Acquisition
Processing
Methodsubtomogram averaging
3 D reconstruction
Algorithmweighted back-projection
SoftwareEM
Detailsexact weighting
Resolution By Author39
Resolution MethodFSC at 0.5 cut-off
Subtomogram Averaging
Number of Subtomograms1911
Applied SymmetryC1 (asymmetric)
Number of Class Averages1
DetailsIndividual particle subvolumes were automatically selected by CCC threshold.
Download
Data from EMDB
Header (meta data in XML format)emd-5224.xml (7.5 KB)
Map dataemd_5224.map.gz (397.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5224
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.4 KB