spacer
spacer

PDBsum entry 1qd7

Go to PDB code: 
Top Page protein ligands links
Ribosome PDB id
1qd7
Jmol
Contents
Protein chains
159 a.a.*
145 a.a.*
97 a.a.*
135 a.a.*
136 a.a.*
85 a.a.*
89 a.a.*
100 a.a.*
Ligands
__N ×359
* C-alpha coords only

References listed in PDB file
Key reference
Title Structure of a bacterial 30s ribosomal subunit at 5.5 a resolution.
Authors W.M.Clemons, J.L.May, B.T.Wimberly, J.P.Mccutcheon, M.S.Capel, V.Ramakrishnan.
Ref. Nature, 1999, 400, 833-840. [DOI no: 10.1038/23631]
PubMed id 10476960
Abstract
The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small-subunit ribosomal RNA to be determined.
Figure 4.
Figure 4 Stereo view of the three-way junction formed by helices 20, 21 and 22 of the central domain of 16S RNA. Inset (right) shows the structure in the context of the 30S subunit. Figure made with RIBBONS50.
Figure 5.
Figure 5 Stereo view of the interactions made by helix 27 of the central domain with helices 24 and 44 of 16S RNA. Inset (right) shows the elements in the whole 30S subunit. Figure made with RIBBONS50.
The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 400, 833-840) copyright 1999.
Secondary reference #1
Title The crystal structure of ribosomal protein s4 reveals a two-Domain molecule with an extensive RNA-Binding surface: one domain shows structural homology to the ets DNA-Binding motif.
Authors C.Davies, R.B.Gerstner, D.E.Draper, V.Ramakrishnan, S.W.White.
Ref. EMBO J, 1998, 17, 4545-4558. [DOI no: 10.1093/emboj/17.16.4545]
PubMed id 9707415
Full text Abstract
Figure 4.
Figure 4 A stereoview of ribosomal protein S4 41 showing the overall distribution of residues believed to be involved in mediating interactions with rRNA. The residues (in standard coloring) are distributed throughout this entire face of the molecule, but can be grouped into three clusters: domain 1 (bottom), domain 2 (top) and the domain interface. The orientation of the molecule is identical to that shown in Figure 2. The figure was produced using MOLSCRIPT (Kraulis, 1991).
Figure 6.
Figure 6 Stereoviews of two significant regions of ribosomal protein S4 41 discussed in the text. (Top) Gln50 within domain 1 has been identified as the site of a point mutation that results in a ram phenotype. It is involved in a hydrogen-bonded interaction with the conserved Arg200, and appears to orient it precisely for interaction with RNA. (Bottom) Arg93 and Arg111 are highly conserved and within the putative RNA-binding site at the domain interface. Conserved Asp95 is mostly buried and appears to orient the adjacent basic residues. A strongly bound sulfate group may reflect the position of a phosphate group when RNA is bound in this region.
The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd
Secondary reference #2
Title The structure of ribosomal protein s5 reveals sites of interaction with 16s rrna.
Authors V.Ramakrishnan, S.W.White.
Ref. Nature, 1992, 358, 768-771. [DOI no: 10.1038/358768a0]
PubMed id 1508272
Abstract
Secondary reference #3
Title Crystal structure of the ribosomal protein s6 from thermus thermophilus.
Authors M.Lindahl, L.A.Svensson, A.Liljas, S.E.Sedelnikova, I.A.Eliseikina, N.P.Fomenkova, N.Nevskaya, S.V.Nikonov, M.B.Garber, T.A.Muranova.
Ref. EMBO J, 1994, 13, 1249-1254.
PubMed id 8137808
Abstract
Secondary reference #4
Title The structure of ribosomal protein s7 at 1.9 a resolution reveals a beta-Hairpin motif that binds double-Stranded nucleic acids.
Authors B.T.Wimberly, S.W.White, V.Ramakrishnan.
Ref. Structure, 1997, 5, 1187-1198. [DOI no: 10.1016/S0969-2126(97)00269-4]
PubMed id 9331418
Full text Abstract
Figure 4.
Figure 4. RNA-binding regions of S7. (a) Electrostatic surface potential of S7. The potential displayed represents a range from -12 to +12 k[B]T, shown with red as negative and blue as positive. The surface potential calculation and display was done using the program GRASP [84]. (b) Ribbon diagram of a similar view, showing residues that are likely to be involved in RNA-binding. Basic residues are shown in blue and solvent-exposed hydrophobic residues are shown in yellow. The red residues R76 and A116 correspond to the sites of crosslinks to 16S RNA. The figure was produced using the program MOLSCRIPT [82].
The above figure is reproduced from the cited reference with permission from Cell Press
Secondary reference #5
Title Crystal structure of ribosomal protein s8 from thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site.
Authors N.Nevskaya, S.Tishchenko, A.Nikulin, S.Al-Karadaghi, A.Liljas, B.Ehresmann, C.Ehresmann, M.Garber, S.Nikonov.
Ref. J Mol Biol, 1998, 279, 233-244. [DOI no: 10.1006/jmbi.1998.1758]
PubMed id 9636713
Full text Abstract
Figure 2.
Figure 2. Schematic representation of the structure of ribosomal protein S8 from T. thermophilus. The Figure was made using MOLSCRIPT (Kraulis, 1991).
The above figure is reproduced from the cited reference with permission from Elsevier
Secondary reference #6
Title Conformational variability of the n-Terminal helix in the structure of ribosomal protein s15.
Authors W.M.Clemons, C.Davies, S.W.White, V.Ramakrishnan.
Ref. Structure, 1998, 6, 429-438. [DOI no: 10.1016/S0969-2126(98)00045-8]
PubMed id 9562554
Full text Abstract
Figure 2.
Figure 2. Overall fold of S15. (a) Stereo view ribbon diagram of S15 with the alternate conformation of the N-terminal helix shown in dark gray. (b) Stereo view Cα trace in the same view as (a) with every tenth residue shown as a small black sphere and labeled; the alternate conformation of the helix is shown in white. (The figures were made using the program MOLSCRIPT [46].)
The above figure is reproduced from the cited reference with permission from Cell Press
Secondary reference #7
Title Solution structure of prokaryotic ribosomal protein s17 by high-Resolution nmr spectroscopy.
Authors T.N.Jaishree, V.Ramakrishnan, S.W.White.
Ref. Biochemistry, 1996, 35, 2845-2853. [DOI no: 10.1021/bi951062i]
PubMed id 8608120
Full text Abstract
 Headers