3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-3izd

Model of the large subunit RNA expansion segment ES27L-out based on a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome. 3IZD is a small part (an expansion segment) which is in an alternative conformation to what is in already 3IZF.

by single particle reconstruction, at 8.6 A resolution

Movie

Orientation:

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1669, Image by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1811, Image by Jmol

#4: With PDB-, Image by Jmol

#5: With PDB-4v6i, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1811 (with PDB-4v6i), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3izd
TitleModel of the large subunit RNA expansion segment ES27L-out based on a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome. 3IZD is a small part (an expansion segment) which is in an alternative conformation to what is in already 3IZF.
Descriptor151-MER
KeywordsRIBOSOME, eukaryotic ribosome, homology modelling, de novo modeling, ribosomal RNA, rRNA, RNA expansion segments
AuthorsArmache, J.-P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soeding, J., Westhof, E., Wilson, D.N., Beckmann, R.
DateDeposition: 2010-10-13, Release: 2010-12-01
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1669, Image by Jmol

#3: Superimposing with simplified surface model of EM map, EMDB-1811, Image by Jmol

#4: With PDB-, Image by Jmol

#5: With PDB-4v6i, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1811 (with PDB-4v6i), Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

Cite: data citing same article

Fit: target map of fitting

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 46, Page 19748-53, Year 2010
TitleCryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
AuthorsJean-Paul Armache, Alexander Jarasch, Andreas M Anger, Elizabeth Villa, Thomas Becker, Shashi Bhushan, Fabrice Jossinet, Michael Habeck, Gülcin Dindar, Sibylle Franckenberg, Viter Marquez, Thorsten Mielke, Michael Thomm, Otto Berninghausen, Birgitta Beatrix, Johannes Söding, Eric Westhof, Daniel N Wilson, Roland Beckmann
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Escherichia coli (metabolism), Eukaryotic Cells (metabolism), Humans, Models, Molecular, Protein Biosynthesis, RNA, Ribosomal (ultrastructure), Ribosomes (chemistry), Saccharomyces cerevisiae (metabolism), Triticum (metabolism)
LinksDOI: 10.1073/pnas.1009999107, PubMed: 20980660, PMC: PMC2993355
Citation - 1
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 46, Page 19754-9, Year 2010
TitleLocalization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
AuthorsJean-Paul Armache, Alexander Jarasch, Andreas M Anger, Elizabeth Villa, Thomas Becker, Shashi Bhushan, Fabrice Jossinet, Michael Habeck, Gülcin Dindar, Sibylle Franckenberg, Viter Marquez, Thorsten Mielke, Michael Thomm, Otto Berninghausen, Birgitta Beatrix, Johannes Söding, Eric Westhof, Daniel N Wilson, Roland Beckmann
KeywordsCryoelectron Microscopy, Eukaryotic Cells (metabolism), Evolution, Molecular, Models, Molecular, Protein Transport, RNA, Ribosomal (chemistry), Ribosomal Proteins (metabolism), Ribosomes (metabolism), Saccharomyces cerevisiae (metabolism), Species Specificity, Triticum (metabolism)
LinksDOI: 10.1073/pnas.1010005107, PubMed: 20974910, PMC: PMC2993421
Components
ID 1 : rRNA expansion segment ES27L in an "out" conformation
Image
DescriptionrRNA expansion segment ES27L in an "out" conformation
Typepolyribonucleotide
Formula weight48721.895 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Common name: yeast
NCBI taxonomy: ID:4932
Organism scientific: Saccharomyces cerevisiae

LinksGenBank: U53879.1, Sequence view
Sample
Sample preparation
pH7.5
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Processing
3D reconstruction
Resolution8.6 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms3044
Nucleic acid atoms3044
Download
PDB format
Allpdb3izd.ent.gz
pdb3izd.ent (uncompressed file)
Header onlypdb3izd.ent.gz
mmCIF format
mmCIF3izd.cif.gz
XML format
All3izd.xml.gz
No-atom3izd-noatom.xml.gz
Ext-atom3izd-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.3 MB
.webm (WebM/VP8 format), 3.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.1 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.8 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.6 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.6 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.4 MB