2ZKR: Structure of a Mammalian Ribosomal 40S Subunit Within an 80S Complex Obtained by Docking Homology Models of the RNA and Proteins Into an 8.7 a Cryo-em MAP

Citation:
Abstract
In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.
MMDB ID: 99595
PDB Deposition Date: 2008/3/27
Updated in MMDB: 2012/08 
Experimental Method:
electron microscopy
Resolution: 8.7  Å
Source Organism:
Similar Structures:
Merged PDB IDs:2ZKQ 2ZKR
Biological Unit for 2ZKR: 86-meric
Molecular Components in 2ZKR
Label Count Molecule
Proteins (50 molecules)
1
40S Ribosomal Protein Rack1
Molecule annotation
1
40S Ribosomal Protein SA
Molecule annotation
1
40S Ribosomal Protein S3E
Molecule annotation
1
40S Ribosomal Protein S9E
Molecule annotation
1
40S Ribosomal Protein S2E
Molecule annotation
1
40S Ribosomal Protein S5E
Molecule annotation
1
40S Ribosomal Protein S15ae
Molecule annotation
1
40S Ribosomal Protein S16e
Molecule annotation
1
40S Ribosomal Protein S20e
Molecule annotation
1
40S Ribosomal Protein S14e
Molecule annotation
1
40S Ribosomal Protein S23e
Molecule annotation
1
40S Ribosomal Protein S18e
Molecule annotation
1
40S Ribosomal Protein S29e
Molecule annotation
1
40S Ribosomal Protein S13e
Molecule annotation
1
40S Ribosomal Protein S11e
Molecule annotation
1
40S Ribosomal Protein S15e
Molecule annotation
1
60S Ribosomal Protein L8
Molecule annotation
1
60S Ribosomal Protein L3
Molecule annotation
1
60S Ribosomal Protein L4
Molecule annotation
1
60S Ribosomal Protein L11
Molecule annotation
1
60S Ribosomal Protein L9
Molecule annotation
1
60S Ribosomal Protein L7A
Molecule annotation
1
60S Acidic Ribosomal Protein P0
Molecule annotation
1
60S Ribosomal Protein L10
Molecule annotation
1
60S Ribosomal Protein L12
Molecule annotation
1
60S Ribosomal Protein L13a
Molecule annotation
1
60S Ribosomal Protein L23
Molecule annotation
1
60S Ribosomal Protein L27a
Molecule annotation
1
60S Ribosomal Protein L15e
Molecule annotation
1
60S Ribosomal Protein L5
Molecule annotation
1
60S Ribosomal Protein L18
Molecule annotation
1
60S Ribosomal Protein L19
Molecule annotation
1
60S Ribosomal Protein L19
Molecule annotation
1
60S Ribosomal Protein L21
Molecule annotation
1
60S Ribosomal Protein L17
Molecule annotation
1
60S Ribosomal Protein L23a
Molecule annotation
1
60S Ribosomal Protein L26
Molecule annotation
1
60S Ribosomal Protein L24
Molecule annotation
1
60S Ribosomal Protein L35
Molecule annotation
1
60S Ribosomal Protein L35
Molecule annotation
1
60S Ribosomal Protein L7
Molecule annotation
1
60S Ribosomal Protein L31
Molecule annotation
1
60S Ribosomal Protein L32
Molecule annotation
1
60S Ribosomal Protein L32
Molecule annotation
1
60S Ribosomal Protein L37a
Molecule annotation
1
60S Ribosomal Protein L37e
Molecule annotation
1
60S Ribosomal Protein L39e
Molecule annotation
1
60S Ribosomal Protein L44e
Molecule annotation
1
60S Ribosomal Protein L10a
Molecule annotation
1
60S Ribosomal Protein L30e
Molecule annotation
Nucleotides(36 molecules)
1
18S Ribosomal RNA
Molecule annotation
1
RNA Expansion Segment ES3
Molecule annotation
1
RNA Expansion Segment ES4
Molecule annotation
1
RNA Expansion Segment ES6 Part I
Molecule annotation
1
RNA Expansion Segment ES6 Part II
Molecule annotation
1
RNA Expansion Segment ES9
Molecule annotation
1
RNA Helix
Molecule annotation
1
RNA Helix
Molecule annotation
1
5.8s Ribosomal RNA
Molecule annotation
1
28S Ribosomal RNA
Molecule annotation
1
RNA Expansion Segment ES3
Molecule annotation
1
RNA Expansion Segment ES4
Molecule annotation
1
RNA Expansion Segment ES5
Molecule annotation
1
RNA Expansion Segment ES7 Part I
Molecule annotation
1
RNA Expansion Segment ES7 Part II
Molecule annotation
1
RNA Expansion Segment ES7 Part III
Molecule annotation
1
RNA Expansion Segment ES9
Molecule annotation
1
RNA Expansion Segment Es12
Molecule annotation
1
RNA Expansion Segment Es15 Part I
Molecule annotation
1
RNA Expansion Segment Es15 Part II
Molecule annotation
1
RNA Expansion Segment Es19
Molecule annotation
1
RNA Expansion Segment Es20
Molecule annotation
1
RNA Expansion Segment Es24
Molecule annotation
1
RNA Expansion Segment Es27
Molecule annotation
1
RNA Expansion Segment Es30
Molecule annotation
1
RNA Expansion Segment Es31 Part I
Molecule annotation
1
RNA Expansion Segment Es31 Part II
Molecule annotation
1
RNA Expansion Segment Es39 Part I
Molecule annotation
1
RNA Expansion Segment Es39 Part II
Molecule annotation
1
RNA Expansion Segment Es39 Part III
Molecule annotation
1
RNA Expansion Segment Es41
Molecule annotation
1
RNA Expansion Segment ES9 Part2
Molecule annotation
1
RNA Expansion Segment Es10
Molecule annotation
1
RNA Helices
Molecule annotation
1
5S Ribosomal RNA
Molecule annotation
1
E Site T-rna
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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