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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

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#1: Depositted 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-3izb, PDB-3ize, PDB-3izf, PDB-3izs, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1811 (with PDB-3izb, PDB-3ize, PDB-3izf, PDB-3izs), 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, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted 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-3izb, PDB-3ize, PDB-3izf, PDB-3izs, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1811 (with PDB-3izb, PDB-3ize, PDB-3izf, PDB-3izs), Image by UCSF CHIMERA

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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
Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
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
Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
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