spacer
spacer

PDBsum entry 1zn1

Go to PDB code: 
protein dna_rna links
Biosynthetic/structural protein/RNA PDB id
1zn1
Jmol
Contents
Protein chains
185 a.a.* *
97 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1zn1
Name: Biosynthetic/structural protein/RNA
Title: Coordinates of rrf fitted into cryo-em map of the 70s post- termination complex
Structure: Ribosomal 23s RNA. Chain: b. Fragment: fragment of large subunit rrna helix 69-71. Ribosomal 16s RNA. Chain: c. Fragment: fragment of small subunit rrna helix 44. Ribosome recycling factor. Chain: a. Synonym: ribosome releasing factor, rrf.
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Authors: N.Gao,A.V.Zavialov,W.Li,J.Sengupta,M.Valle,R.P.Gursky, M.Ehrenberg,J.Frank
Key ref:
N.Gao et al. (2005). Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol Cell, 18, 663-674. PubMed id: 15949441 DOI: 10.1016/j.molcel.2005.05.005
Date:
11-May-05     Release date:   14-Jun-05    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A805  (RRF_ECOLI) -  Ribosome-recycling factor
Seq:
Struc:
185 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12
Seq:
Struc:
124 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     cytoplasmic translational termination   3 terms 
  Biochemical function     protein binding     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.molcel.2005.05.005 Mol Cell 18:663-674 (2005)
PubMed id: 15949441  
 
 
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
N.Gao, A.V.Zavialov, W.Li, J.Sengupta, M.Valle, R.P.Gursky, M.Ehrenberg, J.Frank.
 
  ABSTRACT  
 
Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Interaction of RRF with EF-G and Its Implication for the Disassembly of the Posttermination Complex
Figure 6.
Figure 6. Comparison of Two RRF Conformations on the 70S Posttermination Complex
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 18, 663-674) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20122402 A.V.Pisarev, M.A.Skabkin, V.P.Pisareva, O.V.Skabkina, A.M.Rakotondrafara, M.W.Hentze, C.U.Hellen, and T.V.Pestova (2010).
The role of ABCE1 in eukaryotic posttermination ribosomal recycling.
  Mol Cell, 37, 196-210.  
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.  
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.  
20004164 A.Matsumoto, and H.Ishida (2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
  Structure, 17, 1605-1613.  
19324963 A.Savelsbergh, M.V.Rodnina, and W.Wintermeyer (2009).
Distinct functions of elongation factor G in ribosome recycling and translocation.
  RNA, 15, 772-780.  
19213046 D.M.Hamburg, M.J.Suh, and P.A.Limbach (2009).
Limited proteolysis analysis of the ribosome is affected by subunit association.
  Biopolymers, 91, 410-422.  
19368889 G.Cai, T.Imasaki, Y.Takagi, and F.J.Asturias (2009).
Mediator structural conservation and implications for the regulation mechanism.
  Structure, 17, 559-567.  
19603183 M.O'Connor (2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
  Mol Genet Genomics, 282, 371-380.  
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
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.  
18234219 R.D.Pai, W.Zhang, B.S.Schuwirth, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2008).
Structural Insights into ribosome recycling factor interactions with the 70S ribosome.
  J Mol Biol, 376, 1334-1347.  
18268024 S.C.Abeysirigunawardena, and C.S.Chow (2008).
pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.
  RNA, 14, 782-792.  
18206363 S.Petry, A.Weixlbaumer, and V.Ramakrishnan (2008).
The termination of translation.
  Curr Opin Struct Biol, 18, 70-77.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
18951087 X.Agirrezabala, J.Lei, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, and J.Frank (2008).
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
  Mol Cell, 32, 190-197.  
17956730 A.V.Pisarev, C.U.Hellen, and T.V.Pestova (2007).
Recycling of eukaryotic posttermination ribosomal complexes.
  Cell, 131, 286-299.  
17660830 A.Weixlbaumer, S.Petry, C.M.Dunham, M.Selmer, A.C.Kelley, and V.Ramakrishnan (2007).
Crystal structure of the ribosome recycling factor bound to the ribosome.
  Nat Struct Mol Biol, 14, 733-737.
PDB codes: 2v46 2v47 2v48 2v49
17643374 C.Barat, P.P.Datta, V.S.Raj, M.R.Sharma, H.Kaji, A.Kaji, and R.K.Agrawal (2007).
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
  Mol Cell, 27, 250-261.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
  Proc Natl Acad Sci U S A, 104, 19671-19678.  
17660832 M.A.Borovinskaya, R.D.Pai, W.Zhang, B.S.Schuwirth, J.M.Holton, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2007).
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
  Nat Struct Mol Biol, 14, 727-732.
PDB codes: 2qal 2qam 2qan 2qao 2qb9 2qba 2qbb 2qbc 2qbd 2qbe 2qbf 2qbg 2qbh 2qbi 2qbj 2qbk 2z4k 2z4l 2z4m 2z4n
17564727 M.O'connor (2007).
Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal DeltaA1916 mutation in the 23S rRNA of Escherichia coli.
  Mol Genet Genomics, 278, 307-315.  
17996252 N.Gao, A.V.Zavialov, M.Ehrenberg, and J.Frank (2007).
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
  J Mol Biol, 374, 1345-1358.
PDB code: 2rdo
16891309 A.Liiv, and M.O'Connor (2006).
Mutations in the intersubunit bridge regions of 23 S rRNA.
  J Biol Chem, 281, 29850-29862.  
16556933 A.Pulk, U.Maiväli, and J.Remme (2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
  RNA, 12, 790-796.  
16809861 A.Seshadri, and U.Varshney (2006).
Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3.
  J Biosci, 31, 281-289.  
16487710 G.Hirokawa, N.Demeshkina, N.Iwakura, H.Kaji, and A.Kaji (2006).
The ribosome-recycling step: consensus or controversy?
  Trends Biochem Sci, 31, 143-149.  
16973438 I.K.Ali, L.Lancaster, J.Feinberg, S.Joseph, and H.F.Noller (2006).
Deletion of a conserved, central ribosomal intersubunit RNA bridge.
  Mol Cell, 23, 865-874.  
16689638 K.Mitra, and J.Frank (2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
  Annu Rev Biophys Biomol Struct, 35, 299-317.  
16619019 N.Gao, and J.Frank (2006).
A library of RNA bridges.
  Nat Chem Biol, 2, 231-232.  
16582919 O.Rackham, K.Wang, and J.W.Chin (2006).
Functional epitopes at the ribosome subunit interface.
  Nat Chem Biol, 2, 254-258.  
16272117 B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, and J.H.Cate (2005).
Structures of the bacterial ribosome at 3.5 A resolution.
  Science, 310, 827-834.
PDB codes: 2avy 2aw4 2aw7 2awb
16314459 C.L.Shenvi, K.C.Dong, E.M.Friedman, J.A.Hanson, and J.H.Cate (2005).
Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.
  RNA, 11, 1898-1908.  
16204455 K.Asano, D.Kurita, K.Takada, T.Konno, A.Muto, and H.Himeno (2005).
Competition between trans-translation and termination or elongation of translation.
  Nucleic Acids Res, 33, 5544-5552.  
16307924 K.G.McGarry, S.E.Walker, H.Wang, and K.Fredrick (2005).
Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome.
  Mol Cell, 20, 613-622.  
16199751 N.S.Singh, G.Das, A.Seshadri, R.Sangeetha, and U.Varshney (2005).
Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli.
  Nucleic Acids Res, 33, 5591-5601.  
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.