spacer
spacer

PDBsum entry 1dd3

Go to PDB code: 
protein Protein-protein interface(s) links
Ribosome PDB id
1dd3
Jmol
Contents
Protein chains
128 a.a. *
32 a.a. *
Waters ×247
* Residue conservation analysis
PDB id:
1dd3
Name: Ribosome
Title: Crystal structure of ribosomal protein l12 from thermotoga m
Structure: 50s ribosomal protein l7/l12. Chain: a, b. 50s ribosomal protein l7/l12. Chain: c, d
Source: Thermotoga maritima. Organism_taxid: 2336. Organism_taxid: 2336
Biol. unit: Octamer (from PQS)
Resolution:
2.00Å     R-factor:   0.226     R-free:   0.235
Authors: M.C.Wahl,G.P.Bourenkov,H.D.Bartunik,R.Huber
Key ref:
M.C.Wahl et al. (2000). Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12. EMBO J, 19, 174-186. PubMed id: 10637222 DOI: 10.1093/emboj/19.2.174
Date:
08-Nov-99     Release date:   13-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P29396  (RL7_THEMA) -  50S ribosomal protein L7/L12
Seq:
Struc:
128 a.a.
128 a.a.
Protein chains
Pfam   ArchSchema ?
P29396  (RL7_THEMA) -  50S ribosomal protein L7/L12
Seq:
Struc:
128 a.a.
32 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   3 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     1 term  

 

 
DOI no: 10.1093/emboj/19.2.174 EMBO J 19:174-186 (2000)
PubMed id: 10637222  
 
 
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, R.Huber.
 
  ABSTRACT  
 
Protein L12, the only multicopy component of the ribosome, is presumed to be involved in the binding of translation factors, stimulating factor-dependent GTP hydrolysis. Crystal structures of L12 from Thermotogamaritima have been solved in two space groups by the multiple anomalous dispersion method and refined at 2.4 and 2.0 A resolution. In both crystal forms, an asymmetric unit comprises two full-length L12 molecules and two N-terminal L12 fragments that are associated in a specific, hetero-tetrameric complex with one non-crystallographic 2-fold axis. The two full-length proteins form a tight, symmetric, parallel dimer, mainly through their N-terminal domains. Each monomer of this central dimer additionally associates in a different way with an N-terminal L12 fragment. Both dimerization modes are unlike models proposed previously and suggest that similar complexes may occur in vivo and in situ. The structures also display different L12 monomer conformations, in accord with the suggested dynamic role of the protein in the ribosomal translocation process. The structures have been submitted to the Protein Databank (http://www.rcsb.org/pdb) under accession numbers 1DD3 and 1DD4.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Electrostatic surface potential for the monomer (A), dimer (B) and tetramer (C). A highly acidic surface is visible in the oligomers. The monomer displays several hydrophobic areas, especially in the N-terminal furrow, along the hinge helix and on the underside of the CTD. These patches are efficiently shielded from solvent in the oligomers. Regions used for contacts a–d (Figure 3) are indicated. The figure was produced with GRASP (Nicholls et al., 1991).
Figure 8.
Figure 8 Wire diagram of the core L12 dimer (molecule coloring as in Figure 3) with residues Glu11, Phe29 and Thr32 in space filling mode and the molecular surface indicated as a glassy envelope. The six residues emphasized, critical for the interaction with r-protein L10, line the N-terminal furrows, marking the path of the additional N-terminal fragments (green and yellow). The figure was produced with DINO (http://www.bioz.unibas.ch/~xray/di..).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 174-186) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23385464 S.O.Dahms, M.Kuester, C.Streb, C.Roth, N.Sträter, and M.E.Than (2013).
Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 69, 284-297.  
20385603 K.M.Lee, C.W.Yu, D.S.Chan, T.Y.Chiu, G.Zhu, K.H.Sze, P.C.Shaw, and K.B.Wong (2010).
Solution structure of the dimerization domain of ribosomal protein P2 provides insights for the structural organization of eukaryotic stalk.
  Nucleic Acids Res, 38, 5206-5216.
PDB code: 2w1o
19686666 O.Kurkcuoglu, O.T.Turgut, S.Cansu, R.L.Jernigan, and P.Doruker (2009).
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.
  Biophys J, 97, 1178-1187.  
18936095 T.Miyoshi, T.Nomura, and T.Uchiumi (2009).
Engineering and Characterization of the Ribosomal L10{middle dot}L12 Stalk Complex: A STRUCTURAL ELEMENT RESPONSIBLE FOR HIGH TURNOVER OF THE ELONGATION FACTOR G-DEPENDENT GTPase.
  J Biol Chem, 284, 85-92.  
19084076 V.Briceño, H.Camargo, M.Remacha, C.Santos, and J.P.Ballesta (2009).
Structural and functional characterization of the amino terminal domain of the yeast ribosomal stalk P1 and P2 proteins.
  Int J Biochem Cell Biol, 41, 1315-1322.  
18156682 I.Margiolaki, and J.P.Wright (2008).
Powder crystallography on macromolecules.
  Acta Crystallogr A, 64, 169-180.  
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
18453695 O.Pasternak, A.Bujacz, J.Biesiadka, G.Bujacz, M.Sikorski, and M.Jaskolski (2008).
MAD phasing using the (Ta6Br12)2+ cluster: a retrospective study.
  Acta Crystallogr D Biol Crystallogr, 64, 595-606.
PDB code: 3c0v
18094461 P.Evans, and A.McCoy (2008).
An introduction to molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 64, 1.  
18094462 S.Trapani, and J.Navaza (2008).
AMoRe: classical and modern.
  Acta Crystallogr D Biol Crystallogr, 64, 11-16.  
17397397 T.Naganuma, K.Shiogama, and T.Uchiumi (2007).
The N-terminal regions of eukaryotic acidic phosphoproteins P1 and P2 are crucial for heterodimerization and assembly into the ribosomal GTPase-associated center.
  Genes Cells, 12, 501-510.  
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
  Acta Crystallogr D Biol Crystallogr, 62, 941-945.  
16573688 D.Krokowski, A.Boguszewska, D.Abramczyk, A.Liljas, M.Tchórzewski, and N.Grankowski (2006).
Yeast ribosomal P0 protein has two separate binding sites for P1/P2 proteins.
  Mol Microbiol, 60, 386-400.  
17053098 D.Shcherbakov, M.Dontsova, M.Tribus, M.Garber, and W.Piendl (2006).
Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria.
  Nucleic Acids Res, 34, 5800-5814.  
16373477 R.Schwartz, and J.King (2006).
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure.
  Protein Sci, 15, 102-112.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16292341 A.Savelsbergh, D.Mohr, U.Kothe, W.Wintermeyer, and M.V.Rodnina (2005).
Control of phosphate release from elongation factor G by ribosomal protein L7/12.
  EMBO J, 24, 4316-4323.  
16257826 D.N.Wilson, and K.H.Nierhaus (2005).
Ribosomal proteins in the spotlight.
  Crit Rev Biochem Mol Biol, 40, 243-267.  
15989950 M.Diaconu, U.Kothe, F.Schlünzen, N.Fischer, J.M.Harms, A.G.Tonevitsky, H.Stark, M.V.Rodnina, and M.C.Wahl (2005).
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
  Cell, 121, 991.
PDB codes: 1zav 1zaw 1zax 1zb4
15817456 M.W.Vetting, L.P.de Carvalho, S.L.Roderick, and J.S.Blanchard (2005).
A novel dimeric structure of the RimL Nalpha-acetyltransferase from Salmonella typhimurium.
  J Biol Chem, 280, 22108-22114.
PDB codes: 1s7f 1s7k 1s7l 1s7n
16337596 P.P.Datta, M.R.Sharma, L.Qi, J.Frank, and R.K.Agrawal (2005).
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM.
  Mol Cell, 20, 723-731.
PDB code: 2bcw
14960595 E.V.Bocharov, A.G.Sobol, K.V.Pavlov, D.M.Korzhnev, V.A.Jaravine, A.T.Gudkov, and A.S.Arseniev (2004).
From structure and dynamics of protein L7/L12 to molecular switching in ribosome.
  J Biol Chem, 279, 17697-17706.
PDB codes: 1rqs 1rqt 1rqu 1rqv
15263071 J.Christodoulou, G.Larsson, P.Fucini, S.R.Connell, T.A.Pertinhez, C.L.Hanson, C.Redfield, K.H.Nierhaus, C.V.Robinson, J.Schleucher, and C.M.Dobson (2004).
Heteronuclear NMR investigations of dynamic regions of intact Escherichia coli ribosomes.
  Proc Natl Acad Sci U S A, 101, 10949-10954.  
12409297 C.L.Hanson, P.Fucini, L.L.Ilag, K.H.Nierhaus, and C.V.Robinson (2003).
Dissociation of intact Escherichia coli ribosomes in a mass spectrometer. Evidence for conformational change in a ribosome elongation factor G complex.
  J Biol Chem, 278, 1259-1267.  
12878003 L.C.James, and D.S.Tawfik (2003).
Conformational diversity and protein evolution--a 60-year-old hypothesis revisited.
  Trends Biochem Sci, 28, 361-368.  
12777766 R.Page, S.K.Grzechnik, J.M.Canaves, G.Spraggon, A.Kreusch, P.Kuhn, R.C.Stevens, and S.A.Lesley (2003).
Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome.
  Acta Crystallogr D Biol Crystallogr, 59, 1028-1037.  
11914492 D.Mandelman, P.Gonzalo, J.P.Lavergne, C.Corbier, J.P.Reboud, and R.Haser (2002).
Crystallization and preliminary X-ray study of an N-terminal fragment of rat liver ribosomal P2 protein.
  Acta Crystallogr D Biol Crystallogr, 58, 668-671.  
12235156 F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, and D.Xia (2002).
Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
  J Biol Chem, 277, 46753-46762.
PDB codes: 1mbu 1mbv 1mbx
12377117 G.Michel, V.Sauvé, R.Larocque, Y.Li, A.Matte, and M.Cygler (2002).
The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot.
  Structure, 10, 1303-1315.
PDB code: 1gz0
10913306 J.Zurdo, C.González, J.M.Sanz, M.Rico, M.Remacha, and J.P.Ballesta (2000).
Structural differences between Saccharomyces cerevisiae ribosomal stalk proteins P1 and P2 support their functional diversity.
  Biochemistry, 39, 8935-8943.  
10937868 M.V.Rodnina, H.Stark, A.Savelsbergh, H.J.Wieden, D.Mohr, N.B.Matassova, F.Peske, T.Daviter, C.O.Gualerzi, and W.Wintermeyer (2000).
GTPases mechanisms and functions of translation factors on the ribosome.
  Biol Chem, 381, 377-387.  
11114498 S.Chandra Sanyal, and A.Liljas (2000).
The end of the beginning: structural studies of ribosomal proteins.
  Curr Opin Struct Biol, 10, 633-636.  
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 code is shown on the right.