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PDBsum entry 3i1q

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3i1q
Jmol
Contents
Protein chains
218 a.a. *
206 a.a. *
205 a.a. *
150 a.a. *
100 a.a. *
151 a.a. *
129 a.a. *
127 a.a. *
98 a.a. *
117 a.a. *
123 a.a. *
114 a.a. *
96 a.a. *
88 a.a. *
82 a.a. *
80 a.a. *
55 a.a. *
79 a.a. *
85 a.a. *
51 a.a. *
DNA/RNA
Metals
_MG ×43
Waters ×208
* Residue conservation analysis
PDB id:
3i1q
Name: Ribosome
Title: Crystal structure of the e. Coli 70s ribosome in an intermed of ratcheting
Structure: 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5. Chain: e. 30s ribosomal protein s6.
Source: Escherichia coli k-12. Organism_taxid: 83333. Escherichia coli. Organism_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
3.81Å     R-factor:   0.208     R-free:   0.253
Authors: W.Zhang,J.A.Dunkle,J.H.D.Cate
Key ref:
W.Zhang et al. (2009). Structures of the ribosome in intermediate states of ratcheting. Science, 325, 1014-1017. PubMed id: 19696352 DOI: 10.1126/science.1175275
Date:
27-Jun-09     Release date:   01-Sep-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2
Seq:
Struc:
241 a.a.
218 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3
Seq:
Struc:
233 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5
Seq:
Struc:
167 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P02358  (RS6_ECOLI) -  30S ribosomal protein S6
Seq:
Struc:
135 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P02359  (RS7_ECOLI) -  30S ribosomal protein S7
Seq:
Struc:
179 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8
Seq:
Struc:
130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9
Seq:
Struc:
130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10
Seq:
Struc:
103 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12
Seq:
Struc:
124 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13
Seq:
Struc:
118 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14
Seq:
Struc:
101 a.a.
96 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ4  (RS15_ECOLI) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16
Seq:
Struc:
82 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG63  (RS17_ECOLI) -  30S ribosomal protein S17
Seq:
Struc:
84 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18
Seq:
Struc:
75 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19
Seq:
Struc:
92 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20
Seq:
Struc:
87 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P68679  (RS21_ECOLI) -  30S ribosomal protein S21
Seq:
Struc:
71 a.a.
51 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   7 terms 
  Biological process     cytoplasmic translation   22 terms 
  Biochemical function     structural constituent of ribosome     19 terms  

 

 
DOI no: 10.1126/science.1175275 Science 325:1014-1017 (2009)
PubMed id: 19696352  
 
 
Structures of the ribosome in intermediate states of ratcheting.
W.Zhang, J.A.Dunkle, J.H.Cate.
 
  ABSTRACT  
 
Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.
 
  Selected figure(s)  
 
Figure 1.
View larger version (15K): [in this window] [in a new window] Fig. 1. Rotated states of the ribosome. (A) View of the bacterial 70S ribosome, composed of the small (30S) ribosomal subunit and the large (50S) ribosomal subunit. The small subunit of the ribosome (blue) can rotate from a starting conformation seen in post-initiation and termination states (state R[0], black outline) (12, 13, 18) to a fully rotated conformation seen in elongation, termination, and recycling steps of translation (state R[F], red outline) (1, 15–17). 30S features include the head, platform, and body. The 50S subunit is shown in gray. Letters indicate the positions of the aminoacyl (A), peptidyl (P), and exit (E) tRNA-binding sites. (B) Schematic of tRNA-binding states on the ribosome. In the transition of the ribosome to the fully rotated state, tRNAs shift from binding in the A/A and P/P sites (30S subunit and 50S subunit, respectively) to occupy hybrid binding sites (A/P and P/E for 30S/50S sites). The view of the ribosome is rotated 90° from that in (A). (C) Rotations of the head domain of the small ribosomal subunit. Letters indicate the locations of the aminoacyl (A), peptidyl (P), and exit (E) tRNA binding sites on the large subunit. In state R[0] (black), the head domain is centered over the P site (~0° rotation). Rotations of the head domain toward the E site of up to 14° (red) have been observed (1, 6, 7). The 5' to 3' direction of mRNA, which threads around the neck region of the 30S subunit, is also indicated.
Figure 4.
View larger version (62K): [in this window] [in a new window] Fig. 4. Changes in the position of the head domain in the 30S subunit in state R[2]. (A) Bridge B1 in ribosomes in state R[1] (14). The tRNAs bound in the 30S subunit A site (yellow), and in the P/P (orange) and E/E sites (red), are shown. Domains in protein S13 in the 30S subunit head domain (blue) and protein L5 in the 50S subunit (purple) are marked. An asterisk marks the approximate location of the A-site finger (ASF) helix H38 in 23S rRNA, the tip of which is disordered in the crystal structure (14). Protein L31, not seen in E. coli 70S ribosome structures, has been removed for clarity. (B) Bridge B1 in the apo-70S ribosome in state R[2] (light blue) compared with state R[F] (red). Domains in protein S13 in the 30S subunit head domain and protein L5 in the 50S subunit are marked. Asterisk indicates the same as in (A). (C) Position of full-length tRNAs modeled onto the apo-70S ribosome in state R[2]. The superposition used the head domain of the 30S subunit in the fully rotated state R[F] (16) for reference (1, 11). Surfaces of the modeled tRNAs (yellow and orange) are compared with the position of tRNAs in state R[1] (14), as described in (A), and shown as ribbons. (D) Position of full-length tRNA in the P site of state R[1] (14) modeled onto the ribosome complexed with ASL^Met[f] in the P site in state R[2] (11), with the 30S subunit body and platform of the ribosome in state R[1] used as a reference. Surface of the modeled tRNA (blue) is compared with the position of the P-site ASL^Met[f] in state R[2] (blue), and tRNAs in state R[1] (described above) are shown as ribbons. (E) Stepwise rearrangements in the ribosome along the ratcheting pathway. The molecular envelope of the 30S subunit is shown for clarity. Domains of the 30S subunit (head, body, and platform), tRNA binding sites (A, P, and E, respectively), and bridges B1b, B2a, and B3 are shown. The view is the same as in Fig. 2B. Arrows indicate the direction of movement from one state to the next.
 
  The above figures are reprinted by permission from the AAAs: Science (2009, 325, 1014-1017) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
Functional complexity and regulation through RNA dynamics.
  Nature, 482, 322-330.  
22902368 L.Wang, A.Pulk, M.R.Wasserman, M.B.Feldman, R.B.Altman, J.H.Doudna Cate, and S.C.Blanchard (2012).
Allosteric control of the ribosome by small-molecule antibiotics.
  Nat Struct Mol Biol, 19, 957-963.
PDB codes: 4gaq 4gar 4gas 4gau
21549313 C.Chen, B.Stevens, J.Kaur, D.Cabral, H.Liu, Y.Wang, H.Zhang, G.Rosenblum, Z.Smilansky, Y.E.Goldman, and B.S.Cooperman (2011).
Single-molecule fluorescence measurements of ribosomal translocation dynamics.
  Mol Cell, 42, 367-377.  
21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
  Biophys J, 100, 2201-2208.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
21151095 M.Y.Pavlov, A.Zorzet, D.I.Andersson, and M.Ehrenberg (2011).
Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits.
  EMBO J, 30, 289-301.  
21310988 V.Ramakrishnan (2011).
Molecular biology. The eukaryotic ribosome.
  Science, 331, 681-682.  
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
21124459 A.H.Ratje, J.Loerke, A.Mikolajka, M.Brünner, P.W.Hildebrand, A.L.Starosta, A.Dönhöfer, S.R.Connell, P.Fucini, T.Mielke, P.C.Whitford, J.N.Onuchic, Y.Yu, K.Y.Sanbonmatsu, R.K.Hartmann, P.A.Penczek, D.N.Wilson, and C.M.Spahn (2010).
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
  Nature, 468, 713-716.
PDB codes: 2xsy 2xtg 2xux 2xuy
20588254 A.Korostelev, J.Zhu, H.Asahara, and H.F.Noller (2010).
Recognition of the amber UAG stop codon by release factor RF1.
  EMBO J, 29, 2577-2585.
PDB codes: 3mr8 3mrz 3ms0 3ms1
20855725 B.Llano-Sotelo, J.Dunkle, D.Klepacki, W.Zhang, P.Fernandes, J.H.Cate, and A.S.Mankin (2010).
Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.
  Antimicrob Agents Chemother, 54, 4961-4970.
PDB codes: 1vt2 3or9 3ora 3orb
20192783 C.E.Aitken, A.Petrov, and J.D.Puglisi (2010).
Single ribosome dynamics and the mechanism of translation.
  Annu Rev Biophys, 39, 491-513.  
20562856 C.E.Aitken, and J.D.Puglisi (2010).
Following the intersubunit conformation of the ribosome during translation in real time.
  Nat Struct Mol Biol, 17, 793-800.  
20525967 D.Graber, H.Moroder, J.Steger, K.Trappl, N.Polacek, and R.Micura (2010).
Reliable semi-synthesis of hydrolysis-resistant 3'-peptidyl-tRNA conjugates containing genuine tRNA modifications.
  Nucleic Acids Res, 38, 6796-6802.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20876128 J.A.Dunkle, L.Xiong, A.S.Mankin, and J.H.Cate (2010).
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
  Proc Natl Acad Sci U S A, 107, 17152-17157.
PDB codes: 3oaq 3oar 3oas 3oat 3ofa 3ofb 3ofc 3ofd 3ofo 3ofp 3ofq 3ofr 3ofx 3ofy 3ofz 3og0
20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
  Annu Rev Biochem, 79, 381-412.  
20423978 J.L.Aspden, and R.J.Jackson (2010).
Differential effects of nucleotide analogs on scanning-dependent initiation and elongation of mammalian mRNA translation in vitro.
  RNA, 16, 1130-1137.  
20566885 J.R.Weir, F.Bonneau, J.Hentschel, and E.Conti (2010).
Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.
  Proc Natl Acad Sci U S A, 107, 12139-12144.
PDB code: 2xgj
20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
  Nat Struct Mol Biol, 17, 555-560.
PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20694005 L.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
  Nat Struct Mol Biol, 17, 1072-1078.  
20705654 M.H.Rhodin, and J.D.Dinman (2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
  Nucleic Acids Res, 38, 8377-8389.  
20631791 N.Fischer, A.L.Konevega, W.Wintermeyer, M.V.Rodnina, and H.Stark (2010).
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
  Nature, 466, 329-333.  
20427512 P.C.Whitford, P.Geggier, R.B.Altman, S.C.Blanchard, J.N.Onuchic, and K.Y.Sanbonmatsu (2010).
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
  RNA, 16, 1196-1204.  
20154709 R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, and T.A.Steitz (2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
  Nat Struct Mol Biol, 17, 289-293.
PDB codes: 3knh 3kni 3knj 3knk 3knl 3knm 3knn 3kno
21124925 S.L.Hutson, E.Mui, K.Kinsley, W.H.Witola, M.S.Behnke, K.El Bissati, S.P.Muench, B.Rohrman, S.R.Liu, R.Wollmann, Y.Ogata, A.Sarkeshik, J.R.Yates, and R.McLeod (2010).
T. gondii RP promoters & knockdown reveal molecular pathways associated with proliferation and cell-cycle arrest.
  PLoS One, 5, e14057.  
20541509 T.Kato, H.Yoshida, T.Miyata, Y.Maki, A.Wada, and K.Namba (2010).
Structure of the 100S ribosome in the hibernation stage revealed by electron cryomicroscopy.
  Structure, 18, 719-724.  
20022945 T.Yamamoto, Y.Shimizu, T.Ueda, and Y.Shiro (2010).
Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.
  J Biol Chem, 285, 5646-5652.  
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.  
19833922 A.Liljas (2009).
Biochemistry. Leaps in translational elongation.
  Science, 326, 677-678.  
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.