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PDBsum entry 2zkr

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protein dna_rna ligands Protein-protein interface(s) links
Ribosomal protein/RNA PDB id
2zkr
Jmol
Contents
Protein chains
244 a.a. *
345 a.a. *
257 a.a. *
165 a.a. *
175 a.a. *
120 a.a. *
48 a.a. *
166 a.a. *
74 a.a. *
136 a.a. *
124 a.a. *
122 a.a. *
175 a.a. *
236 a.a. *
120 a.a. *
159 a.a. *
13 a.a. *
96 a.a. *
150 a.a. *
78 a.a. *
110 a.a. *
53 a.a. *
61 a.a. *
158 a.a. *
80 a.a. *
60 a.a. *
58 a.a. *
72 a.a. *
51 a.a. *
48 a.a. *
92 a.a. *
210 a.a. *
113 a.a. *
DNA/RNA
Ligands
ALA-ARG-VAL-LEU-
THR-VAL-ILE-ASN-
GLN-THR
* Residue conservation analysis
PDB id:
2zkr
Name: Ribosomal protein/RNA
Title: Structure of a mammalian ribosomal 60s subunit within an 80s obtained by docking homology models of the RNA and proteins 8.7 a cryo-em map
Structure: 5.8s ribosomal RNA. Chain: 1. 28s ribosomal RNA. Chain: 0. RNA expansion segment es3. Chain: a. Other_details: expansion segment in 5.8s. RNA expansion segment es4. Chain: b.
Source: Canis familiaris. Dog. Organism_taxid: 9615. Other_details: ribosome-channel complexes isolated from er were used to create a 3d map which was used to model the 60 in the 80s ribosome.. Organism_taxid: 9615
Authors: P.Chandramouli,C.W.Akey
Key ref:
P.Chandramouli et al. (2008). Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure, 16, 535-548. PubMed id: 18400176 DOI: 10.1016/j.str.2008.01.007
Date:
27-Mar-08     Release date:   06-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 244 a.a.
Protein chain
No UniProt id for this chain
Struc: 345 a.a.
Protein chain
No UniProt id for this chain
Struc: 257 a.a.
Protein chain
No UniProt id for this chain
Struc: 165 a.a.
Protein chain
No UniProt id for this chain
Struc: 175 a.a.
Protein chain
No UniProt id for this chain
Struc: 120 a.a.
Protein chain
No UniProt id for this chain
Struc: 48 a.a.
Protein chain
No UniProt id for this chain
Struc: 166 a.a.
Protein chain
No UniProt id for this chain
Struc: 74 a.a.
Protein chain
No UniProt id for this chain
Struc: 136 a.a.
Protein chain
No UniProt id for this chain
Struc: 124 a.a.
Protein chain
No UniProt id for this chain
Struc: 122 a.a.
Protein chain
No UniProt id for this chain
Struc: 175 a.a.
Protein chain
No UniProt id for this chain
Struc: 236 a.a.
Protein chain
No UniProt id for this chain
Struc: 120 a.a.
Protein chain
No UniProt id for this chain
Struc: 159 a.a.
Protein chain
No UniProt id for this chain
Struc: 13 a.a.
Protein chain
No UniProt id for this chain
Struc: 96 a.a.
Protein chain
No UniProt id for this chain
Struc: 150 a.a.
Protein chain
No UniProt id for this chain
Struc: 78 a.a.
Protein chain
No UniProt id for this chain
Struc: 110 a.a.
Protein chain
No UniProt id for this chain
Struc: 53 a.a.
Protein chain
No UniProt id for this chain
Struc: 61 a.a.
Protein chain
No UniProt id for this chain
Struc: 158 a.a.
Protein chain
No UniProt id for this chain
Struc: 80 a.a.
Protein chain
No UniProt id for this chain
Struc: 60 a.a.
Protein chain
No UniProt id for this chain
Struc: 58 a.a.
Protein chain
No UniProt id for this chain
Struc: 72 a.a.
Protein chain
No UniProt id for this chain
Struc: 51 a.a.
Protein chain
No UniProt id for this chain
Struc: 48 a.a.
Protein chain
No UniProt id for this chain
Struc: 92 a.a.
Protein chain
No UniProt id for this chain
Struc: 210 a.a.
Protein chain
No UniProt id for this chain
Struc: 113 a.a.
Key:    Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   14 terms 
  Biological process     ribosomal large subunit biogenesis   18 terms 
  Biochemical function     structural constituent of ribosome     6 terms  

 

 
DOI no: 10.1016/j.str.2008.01.007 Structure 16:535-548 (2008)
PubMed id: 18400176  
 
 
Structure of the mammalian 80S ribosome at 8.7 A resolution.
P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, C.W.Akey.
 
  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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A Model of the Cytoplasmic 80S Ribosome
(A) A model of the canine ribosome is shown within a density map of the ribosome-channel complex. The E site tRNA is shown in red between the small (ssu) and large subunits (lsu) of the ribosome. This specimen contained part of the ER translocon (in magenta) that is composed of Sec61 and TRAP. The latter has a prominent lumenal domain (LD).
(B) A molecular model of the canine ribosome is shown in a front view. The subunit rRNAs and conserved proteins are color coded (see boxes). Novel proteins (spheres and rods) and expansion segments (red helices) are also included.
(C) The model of a canine ribosome is shown in a reverse view within the electron microscopy (EM) density map. The position of the ER membrane is indicated by dashed lines.
(D) The molecular model of the canine ribosome is shown in a reverse view.
Figure 7.
Figure 7. Intersubunit Bridges in the Canine Ribosome
(A) Known rotations of the body and head of the small subunit are indicated by arrows on the canine ribosome. Positions of the bridges specific to eukaryotic ribosomes and bridge 2e are indicated.
(B) A reverse view of the ribosome shows that the ebs form a contiguous line along the lateral edge of the small subunit and are also present beneath the subunits (eb11).
(C) An unmodeled C-terminal extension of L37ae contacts h22 in bridge 2e.
(D) An α helix originates from S-IV and extends across the subunit interface to form eb8. Additional density from L7ae and ES31 helps to form this bridge near the L1 stalk helix (H76).
(E) Bridge 9 (eb9) involves extensive interactions between L30e and S13e. The N-terminal helix of S13e is flipped out to interact with protein S-IX.
(F) Protein S-VII forms a bridge between ES3^S and ES41. An icon view in the lower left shows the proximity of eb11 and eb12.
(G) A C-terminal extension of L19e forms a long helix that crosses the intersubunit gap to interact with one branch of ES6^S.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 535-548) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21316217 D.N.Wilson, and R.Beckmann (2011).
The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling.
  Curr Opin Struct Biol, 21, 274-282.  
21400046 Q.Xie, J.Lin, Y.Qin, J.Zhou, and W.Bu (2011).
Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.
  Protein Cell, 2, 161-170.  
20419091 A.Neueder, S.Jakob, G.Pöll, J.Linnemann, R.Deutzmann, H.Tschochner, and P.Milkereit (2010).
A local role for the small ribosomal subunit primary binder rpS5 in final 18S rRNA processing in yeast.
  PLoS One, 5, e10194.  
20562026 D.F.Kelly, D.Dukovski, and T.Walz (2010).
Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy.
  J Mol Biol, 400, 675-681.  
20797628 F.Brandt, L.A.Carlson, F.U.Hartl, W.Baumeister, and K.Grünewald (2010).
The three-dimensional organization of polyribosomes in intact human cells.
  Mol Cell, 39, 560-569.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20159470 J.F.Flanagan, O.Namy, I.Brierley, and R.J.Gilbert (2010).
Direct observation of distinct A/P hybrid-state tRNAs in translocating ribosomes.
  Structure, 18, 257-264.  
20974910 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
  Proc Natl Acad Sci U S A, 107, 19754-19759.
PDB codes: 3iz6 3iz7 3iz9 3izr
20980660 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 107, 19748-19753.
PDB codes: 3izb 3izc 3izd 3ize 3izf 3izs
20688868 K.N.Bulygin, Y.S.Khairulina, P.M.Kolosov, A.G.Ven'yaminova, D.M.Graifer, Y.N.Vorobjev, L.Y.Frolova, L.L.Kisselev, and G.G.Karpova (2010).
Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome.
  RNA, 16, 1902-1914.  
20819938 M.F.O'Donohue, V.Choesmel, M.Faubladier, G.Fichant, and P.E.Gleizes (2010).
Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits.
  J Cell Biol, 190, 853-866.  
20699223 N.Nemoto, C.R.Singh, T.Udagawa, S.Wang, E.Thorson, Z.Winter, T.Ohira, M.Ii, L.Valásek, S.J.Brown, and K.Asano (2010).
Yeast 18 S rRNA is directly involved in the ribosomal response to stringent AUG selection during translation initiation.
  J Biol Chem, 285, 32200-32212.  
20410138 Q.Zeidan, Z.Wang, A.De Maio, and G.W.Hart (2010).
O-GlcNAc cycling enzymes associate with the translational machinery and modify core ribosomal proteins.
  Mol Biol Cell, 21, 1922-1936.  
20118940 T.Schneider-Poetsch, J.Ju, D.E.Eyler, Y.Dang, S.Bhat, W.C.Merrick, R.Green, B.Shen, and J.O.Liu (2010).
Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin.
  Nat Chem Biol, 6, 209-217.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  Hum Genomics, 4, 226-237.  
19850913 B.S.Strunk, and K.Karbstein (2009).
Powering through ribosome assembly.
  RNA, 15, 2083-2104.  
20004163 D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.
  Structure, 17, 1591-1604.
PDB codes: 3jyv 3jyw 3jyx
19129232 E.Babaylova, D.Graifer, A.Malygin, J.Stahl, I.Shatsky, and G.Karpova (2009).
Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome.
  Nucleic Acids Res, 37, 1141-1151.  
20011513 G.Pöll, T.Braun, J.Jakovljevic, A.Neueder, S.Jakob, J.L.Woolford, H.Tschochner, and P.Milkereit (2009).
rRNA maturation in yeast cells depleted of large ribosomal subunit proteins.
  PLoS One, 4, e8249.  
19278647 H.Li, M.S.Wolfe, and D.J.Selkoe (2009).
Toward structural elucidation of the gamma-secretase complex.
  Structure, 17, 326-334.  
20025794 J.Frank (2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
  Q Rev Biophys, 42, 139-158.  
19233204 K.Lasker, M.Topf, A.Sali, and H.J.Wolfson (2009).
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.
  J Mol Biol, 388, 180-194.  
19625386 M.H.Mazauric, J.L.Leroy, K.Visscher, S.Yoshizawa, and D.Fourmy (2009).
Footprinting analysis of BWYV pseudoknot-ribosome complexes.
  RNA, 15, 1775-1786.  
19073700 P.H.Too, M.K.Ma, A.N.Mak, Y.T.Wong, C.K.Tung, G.Zhu, S.W.Au, K.B.Wong, and P.C.Shaw (2009).
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
  Nucleic Acids Res, 37, 602-610.
PDB codes: 2jdl 2jjr 2vs6
19223173 S.C.Blanchard (2009).
Single-molecule observations of ribosome function.
  Curr Opin Struct Biol, 19, 103-109.  
19432457 S.P.Edmondson, J.Turri, K.Smith, A.Clark, and J.W.Shriver (2009).
Structure, stability, and flexibility of ribosomal protein L14e from Sulfolobus solfataricus.
  Biochemistry, 48, 5553-5562.  
19286367 Y.Cheng (2009).
Toward an atomic model of the 26S proteasome.
  Curr Opin Struct Biol, 19, 203-208.  
19489732 Y.Cheng, and T.Walz (2009).
The advent of near-atomic resolution in single-particle electron microscopy.
  Annu Rev Biochem, 78, 723-742.  
19019145 J.C.Chiou, X.P.Li, M.Remacha, J.P.Ballesta, and N.E.Tumer (2008).
The ribosomal stalk is required for ribosome binding, depurination of the rRNA and cytotoxicity of ricin A chain in Saccharomyces cerevisiae.
  Mol Microbiol, 70, 1441-1452.  
18611385 J.F.Ménétret, R.S.Hegde, M.Aguiar, S.P.Gygi, E.Park, T.A.Rapoport, and C.W.Akey (2008).
Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.
  Structure, 16, 1126-1137.
PDB code: 3dkn
18824510 M.L.Powell, S.Napthine, R.J.Jackson, I.Brierley, and T.D.Brown (2008).
Characterization of the termination-reinitiation strategy employed in the expression of influenza B virus BM2 protein.
  RNA, 14, 2394-2406.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.