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PDBsum entry 1vsp
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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
1vsp

 

 

 

 

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Contents
Protein chains
127 a.a. *
272 a.a. *
201 a.a. *
194 a.a. *
180 a.a. *
173 a.a. *
148 a.a. *
138 a.a. *
122 a.a. *
146 a.a. *
137 a.a. *
118 a.a. *
106 a.a. *
137 a.a. *
117 a.a. *
101 a.a. *
109 a.a. *
92 a.a. *
103 a.a. *
185 a.a. *
76 a.a. *
88 a.a. *
62 a.a. *
60 a.a. *
56 a.a. *
48 a.a. *
63 a.a. *
35 a.a. *
DNA/RNA
* Residue conservation analysis
Obsolete entry
PDB id:
1vsp
Name: Ribosome
Title: Interactions and dynamics of the shine-dalgarno helix in the 70s ribosome. This file, 1vsp, contains the 50s ribosome subunit. 30s ribosome subunit is in the file 2qnh
Structure: 23s large subunit ribosomal RNA. Chain: w. 5s large subunit ribosomal RNA. Chain: x. 50s ribosomal protein l1. Chain: a. 50s ribosomal protein l2. Chain: b. 50s ribosomal protein l3.
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Strain: hb27
Resolution:
3.83Å     R-factor:   0.327     R-free:   0.351
Authors: A.Korostelev,S.Trakhanov,H.Asahara,M.Laurberg,H.F.Noller
Key ref:
A.Korostelev et al. (2007). Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome. Proc Natl Acad Sci U S A, 104, 16840-16843. PubMed id: 17940016 DOI: 10.1073/pnas.0707850104
Date:
18-Jul-07     Release date:   13-Nov-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q72GV9  (RL1_THET2) -  50S ribosomal protein L1 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		229 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I07  (RL2_THET2) -  50S ribosomal protein L2 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		276 a.a.
272 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I04  (RL3_THET2) -  50S ribosomal protein L3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		206 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I05  (RL4_THET2) -  50S ribosomal protein L4 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		205 a.a.
194 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I16  (RL5_THET2) -  50S ribosomal protein L5 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		182 a.a.
180 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I19  (RL6_THET2) -  50S ribosomal protein L6 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		180 a.a.
173 a.a.
Protein chain
Pfam   ArchSchema ?
Q72GV5  (RL9_THET2) -  50S ribosomal protein L9 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		148 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IN1  (RL13_THET2) -  50S ribosomal protein L13 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		140 a.a.
138 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72I14  (RL14_THET2) -  50S ribosomal protein L14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I23  (RL15_THET2) -  50S ribosomal protein L15 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I11  (RL16_THET2) -  50S ribosomal protein L16 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		141 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I33  (RL17_THET2) -  50S ribosomal protein L17 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		118 a.a.
118 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I20  (RL18_THET2) -  50S ribosomal protein L18 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		112 a.a.
106 a.a.
Protein chain
Pfam   ArchSchema ?
Q72JU9  (RL19_THET2) -  50S ribosomal protein L19 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		146 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L76  (RL20_THET2) -  50S ribosomal protein L20 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR2  (RL21_THET2) -  50S ribosomal protein L21 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I09  (RL22_THET2) -  50S ribosomal protein L22 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		113 a.a.
109 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I06  (Q72I06_THET2) -  50S ribosomal protein L23 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		96 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I15  (RL24_THET2) -  50S ribosomal protein L24 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		110 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IA7  (RL25_THET2) -  50S ribosomal protein L25 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		206 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR3  (RL27_THET2) -  50S ribosomal protein L27 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		85 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
Q72G84  (Q72G84_THET2) -  50S ribosomal protein L28 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		98 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I12  (RL29_THET2) -  50S ribosomal protein L29 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		72 a.a.
62 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I22  (Q72I22_THET2) -  50S ribosomal protein L30 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		60 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P62652  (RL32_THET2) -  50S ribosomal protein L32 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		60 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		49 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L77  (RL35_THET2) -  50S ribosomal protein L35 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		65 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I28  (RL36_THET2) -  50S ribosomal protein L36 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		37 a.a.
35 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  G-G-U-C-A-A-G-A-U-G-G-U-A-A-G-G-G-C-C-C-A-C-G-G-U-G-G-A-U-G-C-C-U-C-G-G-C-A-C- ... 2889 bases
  U-C-C-C-C-C-G-U-G-C-C-C-A-U-A-G-C-G-G-C-G-U-G-G-A-A-C-C-A-C-C-C-G-U-U-C-C-C-A- 120 bases

 

 
DOI no: 10.1073/pnas.0707850104 Proc Natl Acad Sci U S A 104:16840-16843 (2007)
PubMed id: 17940016  
 
 
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
A.Korostelev, S.Trakhanov, H.Asahara, M.Laurberg, L.Lancaster, H.F.Noller.
 
  ABSTRACT  
 
The crystal structure of an initiation-like 70S ribosome complex containing an 8-bp Shine-Dalgarno (SD) helix was determined at 3.8-A resolution. Translation-libration-screw analysis showed that the inherent anisotropic motions of the SD helix were biased along its helical axis, suggesting that during the first step of translocation, the SD helix moves along its helical screw axis. Contacts between the SD helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of 16S rRNA. Contact with the neck (helix 28) of the 30S subunit near its hinge point suggests that formation of the SD helix could affect positioning of the head of the 30S subunit for optimal interaction with initiator tRNA. The bulged U723 in helix 23a interacts with the minor groove of the SD helix at the C1539.G-10 base pair, explaining its selective conservation in bacteria and archaea.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure and dynamics of the SD helix. (a) (Upper) Nucleotide sequences and base pairing between mRNA and 16S rRNA in the initiation-like 70S ribosome complex. SD sequence, initiator codon, and anti-SD sequences are shown in bold; shaded nucleotides are disordered in the refined x-ray structure. (Lower) Stereoview of the fit of the SD helix to a composite omit density map calculated with [A]-weighted (2F[o] – F[c]) coefficients contoured at 1.2 . (b) Stereoview of the nonintersecting screw axes (blue) for the SD helix (yellow). The length of each axis is proportional to its respective mean-square displacement value. The primary screw axis is indicated by a rotational arrow. (c) Thermal ellipsoid representation of the librational motions of the SD helix around the dominant screw axis coinciding with the SD helical axis. Atomic displacement parameters for the SD helix calculated from the TLS model are colored according to the magnitude of the displacements, increasing from blue (smallest) to red (largest). The view is from the upstream end of the helix. 		Figure 3.
Fig. 3. Interactions of the SD helix with the ribosome. (a) Location of the SD helix (yellow) relative to the structure of 16S rRNA in the 70S ribosome initiation-like complex. Helices 23a, 26, and 28, which contact the SD helix, are rendered in dark blue ribbon representations, and the SD helix is shown in yellow. (b) Interactions of the SD helix with helices 23a, 26, and 28 of 16S rRNA. The P-site tRNA is shown in orange. (c) Secondary structure of T. thermophilus 16S rRNA, showing in bold the anti-SD region at the 3' end and structural features (helices 23a, 26, and 28) that interact with the SD helix.
 
  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.  
21205638 J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, and N.Ban (2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science, 331, 730-736.
PDB codes: 2xzm 2xzn
21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (2011).
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
  Proc Natl Acad Sci U S A, 108, 1839-1844.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
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
19952067 K.Réblová, F.Rázga, W.Li, H.Gao, J.Frank, and J.Sponer (2010).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
  Nucleic Acids Res, 38, 1325-1340.  
  21304717 M.von Jan, A.Lapidus, T.G.Del Rio, A.Copeland, H.Tice, J.F.Cheng, S.Lucas, F.Chen, M.Nolan, L.Goodwin, C.Han, S.Pitluck, K.Liolios, N.Ivanova, K.Mavromatis, G.Ovchinnikova, O.Chertkov, A.Pati, A.Chen, K.Palaniappan, M.Land, L.Hauser, Y.J.Chang, C.D.Jeffries, E.Saunders, T.Brettin, J.C.Detter, P.Chain, K.Eichinger, H.Huber, S.Spring, M.Rohde, M.Göker, R.Wirth, T.Woyke, J.Bristow, J.A.Eisen, V.Markowitz, P.Hugenholtz, N.C.Kyrpides, and H.P.Klenk (2010).
Complete genome sequence of Archaeoglobus profundus type strain (AV18).
  Stand Genomic Sci, 2, 327-346.  
19706509 A.C.Lamanna, and K.Karbstein (2009).
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.
  Proc Natl Acad Sci U S A, 106, 14259-14264.  
19095617 A.Devaraj, S.Shoji, E.D.Holbrook, and K.Fredrick (2009).
A role for the 30S subunit E site in maintenance of the translational reading frame.
  RNA, 15, 255-265.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19706445 C.Tu, X.Zhou, J.E.Tropea, B.P.Austin, D.S.Waugh, D.L.Court, and X.Ji (2009).
Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis.
  Proc Natl Acad Sci U S A, 106, 14843-14848.
PDB codes: 3ieu 3iev
19154330 D.Qin, and K.Fredrick (2009).
Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA.
  Mol Microbiol, 71, 1239-1249.  
19647434 J.B.Munro, K.Y.Sanbonmatsu, C.M.Spahn, and S.C.Blanchard (2009).
Navigating the ribosome's metastable energy landscape.
  Trends Biochem Sci, 34, 390-400.  
19486296 T.Tenson, and V.Hauryliuk (2009).
Does the ribosome have initiation and elongation modes of translation?
  Mol Microbiol, 72, 1310-1315.  
19545171 X.Shi, K.Chiu, S.Ghosh, and S.Joseph (2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
  Biochemistry, 48, 6772-6782.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18464793 A.V.Pisarev, V.G.Kolupaeva, M.M.Yusupov, C.U.Hellen, and T.V.Pestova (2008).
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes.
  EMBO J, 27, 1609-1621.  
18497739 M.Y.Pavlov, A.Antoun, M.Lovmar, and M.Ehrenberg (2008).
Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting.
  EMBO J, 27, 1706-1717.  
19029596 O.Kurkcuoglu, P.Doruker, T.Z.Sen, A.Kloczkowski, and R.L.Jernigan (2008).
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
  Phys Biol, 5, 046005.  
18953726 S.Marzi, P.Fechter, C.Chevalier, P.Romby, and T.Geissmann (2008).
RNA switches regulate initiation of translation in bacteria.
  Biol Chem, 389, 585-598.  
18667704 V.Di Giacco, V.Márquez, Y.Qin, M.Pech, F.J.Triana-Alonso, D.N.Wilson, and K.H.Nierhaus (2008).
Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG.
  Proc Natl Acad Sci U S A, 105, 10715-10720.  
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.

 

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