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PDBsum entry 2qa4
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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
2qa4

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
237 a.a. *
337 a.a. *
246 a.a. *
140 a.a. *
172 a.a. *
119 a.a. *
125 a.a. *
160 a.a. *
118 a.a. *
142 a.a. *
132 a.a. *
145 a.a. *
194 a.a. *
186 a.a. *
115 a.a. *
143 a.a. *
95 a.a. *
150 a.a. *
81 a.a. *
119 a.a. *
53 a.a. *
65 a.a. *
154 a.a. *
82 a.a. *
142 a.a. *
73 a.a. *
56 a.a. *
46 a.a. *
92 a.a. *
DNA/RNA
Metals
_CL ×22
_NA ×86
_MG ×116
_CD ×5
__K ×2
* Residue conservation analysis
PDB id:
2qa4
Name: Ribosome
Title: A more complete structure of the the l7/l12 stalk of the haloarcula marismortui 50s large ribosomal subunit
Structure: 23s ribosomal RNA. Chain: 0. 5s ribosomal RNA. Chain: 9. 50s ribosomal protein l2p. Chain: a. 50s ribosomal protein l3p. Chain: b. 50s ribosomal protein l4p.
Source: Haloarcula marismortui. Organism_taxid: 2238. Organism_taxid: 2238
Resolution:
3.00Å     R-factor:   0.241     R-free:   0.288
Authors: T.A.Steitz,J.M.Kavran
Key ref:
J.M.Kavran and T.A.Steitz (2007). Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J Mol Biol, 371, 1047-1059. PubMed id: 17599351 DOI: 10.1016/j.jmb.2007.05.091
Date:
14-Jun-07     Release date:   01-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  Large ribosomal subunit protein uL2 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		240 a.a.
237 a.a.
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  Large ribosomal subunit protein uL3 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  Large ribosomal subunit protein uL4 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  Large ribosomal subunit protein uL5 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  Large ribosomal subunit protein uL6 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  Large ribosomal subunit protein eL8 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P15825  (RL10_HALMA) -  Large ribosomal subunit protein uL10 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		348 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P60617  (RL10E_HALMA) -  Large ribosomal subunit protein uL16 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
160 a.a.*
Protein chain
Pfam   ArchSchema ?
P14122  (RL11_HALMA) -  Large ribosomal subunit protein uL11 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		162 a.a.
118 a.a.
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  Large ribosomal subunit protein uL13 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  Large ribosomal subunit protein uL14 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		132 a.a.
132 a.a.*
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  Large ribosomal subunit protein uL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  Large ribosomal subunit protein eL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  Large ribosomal subunit protein uL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  Large ribosomal subunit protein eL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19E_HALMA) -  Large ribosomal subunit protein eL19 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		149 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  Large ribosomal subunit protein eL21 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  Large ribosomal subunit protein uL22 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  Large ribosomal subunit protein uL23 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  Large ribosomal subunit protein uL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  Large ribosomal subunit protein eL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  Large ribosomal subunit protein uL29 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  Large ribosomal subunit protein uL30 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  Large ribosomal subunit protein eL31 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  Large ribosomal subunit protein eL32 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  Large ribosomal subunit protein eL43 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  Large ribosomal subunit protein eL37 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  Large ribosomal subunit protein eL39 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		50 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P32411  (RL44E_HALMA) -  Large ribosomal subunit protein eL42 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

DNA/RNA chains
  U-A-U-G-C-C-A-G-C-U-G-G-U-G-G-A-U-U-G-C-U-C-G-G-C-U-C-A-G-G-C-G-C-U-G-A-U-G-A- ... 2753 bases
  U-U-A-G-G-C-G-G-C-C-A-C-A-G-C-G-G-U-G-G-G-G-U-U-G-C-C-U-C-C-C-G-U-A-C-C-C-A-U- 122 bases

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.jmb.2007.05.091 J Mol Biol 371:1047-1059 (2007)
PubMed id: 17599351  
 
 
Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements.
J.M.Kavran, T.A.Steitz.
 
  ABSTRACT  
 
Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Interfaces between stalk components of the large ribosomal subunit. (a) A bifurcated stalk is formed on H43/44 RNA (red, space fill) with one lobe formed by L10 (green, ribbons) and one lobe formed by L11 (yellow, ribbons). The L11 NTD is extending away from the ribosome. (b) The N-terminal extension of L10 recognizes A1150 of 23 S RNA through interactions with Ile12 and Arg69. (c) The interactions between L10 and L11 are minimal and stabilized by each proteins respective interactions with the stalk RNA. 		Figure 3.
Figure 3. Unassigned electron density with alpha-helical proportions. A stereo image of a difference Fourier map calculated between 50–4 Å resolution and contoured at 2 σ using F[o] amplitudes from NAC soaked ribosome crystals and F[c] amplitudes calculated from the model containing the newly built base of the stalk. The unassigned density (orange) has α-helical proportions and occupies a position near the C terminus of L10 NTD (green, ribbons).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 1047-1059) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
20507916 I.Besseová, K.Réblová, N.B.Leontis, and J.Sponer (2010).
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
  Nucleic Acids Res, 38, 6247-6264.  
20018246 N.R.Voss, D.Lyumkis, A.Cheng, P.W.Lau, A.Mulder, G.C.Lander, E.J.Brignole, D.Fellmann, C.Irving, E.L.Jacovetty, A.Leung, J.Pulokas, J.D.Quispe, H.Winkler, C.Yoshioka, B.Carragher, and C.S.Potter (2010).
A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.
  J Struct Biol, 169, 389-398.  
19702336 J.L.Miller, H.Cimen, H.Koc, and E.C.Koc (2009).
Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.
  J Proteome Res, 8, 4789-4798.  
19225518 K.Bokov, and S.V.Steinberg (2009).
A hierarchical model for evolution of 23S ribosomal RNA.
  Nature, 457, 977-980.  
19797078 K.Y.Lo, Z.Li, F.Wang, E.M.Marcotte, and A.W.Johnson (2009).
Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0.
  J Cell Biol, 186, 849-862.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
18611379 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.
  Structure, 16, 1059-1066.
PDB codes: 3cjq 3cjr 3cjs 3cjt 3cju 3egv
18493745 J.Soppa, A.Baumann, M.Brenneis, M.Dambeck, O.Hering, and C.Lange (2008).
Genomics and functional genomics with haloarchaea.
  Arch Microbiol, 190, 197-215.  
18957331 K.B.Hall (2008).
RNA in motion.
  Curr Opin Chem Biol, 12, 612-618.  
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
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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