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PDBsum entry 1eg0

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protein dna_rna ligands links
Ribosome PDB id
1eg0
Jmol
Contents
Protein chains
159 a.a.* *
145 a.a.* *
97 a.a.* *
135 a.a.* *
136 a.a.* *
88 a.a.* *
89 a.a.* *
100 a.a.* *
220 a.a.* *
164 a.a.* *
133 a.a.* *
DNA/RNA
Ligands
__N ×33
* Residue conservation analysis
* C-alpha coords only
PDB id:
1eg0
Name: Ribosome
Title: Fitting of components with known structure into an 11.5 a cryo-em map of the e.Coli 70s ribosome
Structure: Fragment of 16s rrna helix 23. Chain: i. Fragment: residues 673-713. Other_details: modeled as analogous fragment of t. Thermophilus taken from PDB entry 1qd7. Fragment of 23s rrna. Chain: l. Fragment: residues 1051-1108. Other_details: t. Maritima RNA sequence and model taken
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Authors: I.S.Gabashvili,R.K.Agrawal,C.M.T.Spahn,R.A.Grassucci, D.I.Svergun,J.Frank,P.Penczek
Key ref:
I.S.Gabashvili et al. (2000). Solution structure of the E. coli 70S ribosome at 11.5 A resolution. Cell, 100, 537-549. PubMed id: 10721991 DOI: 10.1016/S0092-8674(00)80690-X
Date:
11-Feb-00     Release date:   06-Mar-00    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P81288  (RS4_GEOSE) -  30S ribosomal protein S4
Seq:
Struc:
200 a.a.
159 a.a.*
Protein chain
Pfam   ArchSchema ?
P02357  (RS5_GEOSE) -  30S ribosomal protein S5
Seq:
Struc:
166 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P23370  (RS6_THETH) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
135 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P80378  (RS15_THETH) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P23828  (RS17_GEOSE) -  30S ribosomal protein S17
Seq:
Struc:
87 a.a.
89 a.a.*
Protein chain
No UniProt id for this chain
Struc: 100 a.a.
Protein chain
Pfam   ArchSchema ?
P27150  (RL1_THETH) -  50S ribosomal protein L1
Seq:
Struc:
229 a.a.
220 a.a.
Protein chain
Pfam   ArchSchema ?
P02391  (RL6_GEOSE) -  50S ribosomal protein L6
Seq:
Struc:
178 a.a.
164 a.a.
Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
Seq:
Struc:
141 a.a.
133 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     regulation of translation   2 terms 
  Biochemical function     structural constituent of ribosome     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)80690-X Cell 100:537-549 (2000)
PubMed id: 10721991  
 
 
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
I.S.Gabashvili, R.K.Agrawal, C.M.Spahn, R.A.Grassucci, D.I.Svergun, J.Frank, P.Penczek.
 
  ABSTRACT  
 
Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The 11.5 Å Resolution Cryo-EM Map of the E. coli 70S RibosomeThe cryo-EM map is shown in (a) subunit–subunit side view, (b) 30S subunit solvent–side view, (c) top view, and (d) the 50S subunit solvent–side view. Domains and features of the 30S subunit (yellow, with helix 44 shown in red) and 50S subunit (blue) are as follows: b, body; h, head; pt, platform; sp, spur; sh, shoulder; St, stalk base; L1, protein L1; and CP, central protuberance. * and # mark sites of the shoulder contacting the head in Cate et al., 1999. V marks the v-shaped structure possibly representing helices of the 5S rRNA. Inset (upper left) displays cryo-EM map of the fMet-tRNA[f]^Met (green), with arrows pointing to sites interacting with ribosomal components (left), and the expected appearance of fMet-tRNA[f]^Met ([51]) at vert, similar 10 Å resolution (right).
Figure 4.
Figure 4. Examples for Fittings of Proteins into the Cryo-EM Density MapFittings of protein crystal structures (carbon backbones) into the cryo-EM density (white, wire-mesh), displayed in stereo. Top, S5 ([49]); center, S6 ( [38]); bottom, S7 ( [31 and 59]). These protein structures are displayed on the 30S subunit map in Figure 5 in corresponding colors.
 
  The above figures are reprinted by permission from Cell Press: Cell (2000, 100, 537-549) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23142985 B.J.Greber, D.Boehringer, C.Montellese, and N.Ban (2012).
Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit.
  Nat Struct Mol Biol, 19, 1228-1233.
PDB codes: 4b6a 4b6b
20888470 C.L.Lawson (2010).
Unified data resource for cryo-EM.
  Methods Enzymol, 483, 73-90.  
20637413 H.Y.Liao, and J.Frank (2010).
Definition and estimation of resolution in single-particle reconstructions.
  Structure, 18, 768-775.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20584915 J.Sengupta, C.Bussiere, J.Pallesen, M.West, A.W.Johnson, and J.Frank (2010).
Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit.
  J Cell Biol, 189, 1079-1086.  
19965869 M.R.Sharma, A.Dönhöfer, C.Barat, V.Marquez, P.P.Datta, P.Fucini, D.N.Wilson, and R.K.Agrawal (2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
  J Biol Chem, 285, 4006-4014.  
20541509 T.Kato, H.Yoshida, T.Miyata, Y.Maki, A.Wada, and K.Namba (2010).
Structure of the 100S ribosome in the hibernation stage revealed by electron cryomicroscopy.
  Structure, 18, 719-724.  
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.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19217333 C.M.Clemson, J.N.Hutchinson, S.A.Sara, A.W.Ensminger, A.H.Fox, A.Chess, and J.B.Lawrence (2009).
An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles.
  Mol Cell, 33, 717-726.  
19167328 F.Brandt, S.A.Etchells, J.O.Ortiz, A.H.Elcock, F.U.Hartl, and W.Baumeister (2009).
The native 3D organization of bacterial polysomes.
  Cell, 136, 261-271.  
19897894 H.J.Ha, W.S.Song, H.M.Kim, H.S.Son, and K.Lee (2009).
Functional study of the residue C899 in the 900 tetraloop of Escherichia coli small subunit ribosomal RNA.
  Biosci Biotechnol Biochem, 73, 2544-2546.  
19804732 J.Curuksu, J.Sponer, and M.Zacharias (2009).
Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations.
  Biophys J, 97, 2004-2013.  
20025794 J.Frank (2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
  Q Rev Biophys, 42, 139-158.  
19580754 M.Han, Y.Mei, H.Khant, and S.J.Ludtke (2009).
Characterization of antibiotic peptide pores using cryo-EM and comparison to neutron scattering.
  Biophys J, 97, 164-172.  
19497863 M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, and R.K.Agrawal (2009).
Structure of a mitochondrial ribosome with minimal RNA.
  Proc Natl Acad Sci U S A, 106, 9637-9642.
PDB codes: 3iy8 3iy9
19166941 M.Shatsky, R.J.Hall, S.E.Brenner, and R.M.Glaeser (2009).
A method for the alignment of heterogeneous macromolecules from electron microscopy.
  J Struct Biol, 166, 67-78.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
19683579 Z.Lu, T.R.Shaikh, D.Barnard, X.Meng, H.Mohamed, A.Yassin, C.A.Mannella, R.K.Agrawal, T.M.Lu, and T.Wagenknecht (2009).
Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy.
  J Struct Biol, 168, 388-395.  
18611858 D.Piekna-Przybylska, P.Przybylski, A.Baudin-Baillieu, J.P.Rousset, and M.J.Fournier (2008).
Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit.
  J Biol Chem, 283, 26026-26036.  
18286627 J.B.Munro, A.Vaiana, K.Y.Sanbonmatsu, and S.C.Blanchard (2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.
  Biopolymers, 89, 565-577.  
18468905 J.Heredia-Moya, and K.L.Kirk (2008).
Synthesis of beta-(S-methyl)thioaspartic acid and derivatives.
  Bioorg Med Chem, 16, 5908-5913.  
18606549 J.LeBarron, R.A.Grassucci, T.R.Shaikh, W.T.Baxter, J.Sengupta, and J.Frank (2008).
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.
  J Struct Biol, 164, 24-32.  
18637734 K.Bakowska-Zywicka, A.M.Kietrys, and T.Twardowski (2008).
Antisense oligonucleotides targeting universally conserved 26S rRNA domains of plant ribosomes at different steps of polypeptide elongation.
  Oligonucleotides, 18, 175-186.  
18199747 M.Cottevieille, E.Larquet, S.Jonic, M.V.Petoukhov, G.Caprini, S.Paravisi, D.I.Svergun, M.A.Vanoni, and N.Boisset (2008).
The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications.
  J Biol Chem, 283, 8237-8249.
PDB code: 2vdc
18299206 M.F.Schmid, and C.R.Booth (2008).
Methods for aligning and for averaging 3D volumes with missing data.
  J Struct Biol, 161, 243-248.  
18971332 P.Julián, A.L.Konevega, S.H.Scheres, M.Lázaro, D.Gil, W.Wintermeyer, M.V.Rodnina, and M.Valle (2008).
Structure of ratcheted ribosomes with tRNAs in hybrid states.
  Proc Natl Acad Sci U S A, 105, 16924-16927.  
18755836 R.Ero, L.Peil, A.Liiv, and J.Remme (2008).
Identification of pseudouridine methyltransferase in Escherichia coli.
  RNA, 14, 2223-2233.  
19094041 S.Jonić, C.O.Sorzano, and N.Boisset (2008).
Comparison of single-particle analysis and electron tomography approaches: an overview.
  J Microsc, 232, 562-579.  
18534866 S.M.Stagg, G.C.Lander, J.Quispe, N.R.Voss, A.Cheng, H.Bradlow, S.Bradlow, B.Carragher, and C.S.Potter (2008).
A test-bed for optimizing high-resolution single particle reconstructions.
  J Struct Biol, 163, 29-39.  
18805973 T.Monshupanee, S.T.Gregory, S.Douthwaite, W.Chungjatupornchai, and A.E.Dahlberg (2008).
Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications.
  J Bacteriol, 190, 7754-7761.  
19180078 T.R.Shaikh, H.Gao, W.T.Baxter, F.J.Asturias, N.Boisset, A.Leith, and J.Frank (2008).
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
  Nat Protoc, 3, 1941-1974.  
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.  
17369838 A.L.Konevega, N.Fischer, Y.P.Semenkov, H.Stark, W.Wintermeyer, and M.V.Rodnina (2007).
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
  Nat Struct Mol Biol, 14, 318-324.  
17683199 A.L.Manuell, J.Quispe, and S.P.Mayfield (2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
  PLoS Biol, 5, e209.  
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.  
17611751 C.O.Sorzano, S.Jonic, M.Cottevieille, E.Larquet, N.Boisset, and S.Marco (2007).
3D electron microscopy of biological nanomachines: principles and applications.
  Eur Biophys J, 36, 995.  
18075576 C.V.Robinson, A.Sali, and W.Baumeister (2007).
The molecular sociology of the cell.
  Nature, 450, 973-982.  
17446867 D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, and J.Frank (2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
  EMBO J, 26, 2421-2431.
PDB codes: 2p8w 2p8x 2p8y 2p8z
17553840 F.Rázga, J.Koca, A.Mokdad, and J.Sponer (2007).
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.
  Nucleic Acids Res, 35, 4007-4017.  
17088492 G.Hirokawa, H.Kaji, and A.Kaji (2007).
Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin.
  Antimicrob Agents Chemother, 51, 175-180.  
17540173 H.Gao, Z.Zhou, U.Rawat, C.Huang, L.Bouakaz, C.Wang, Z.Cheng, Y.Liu, A.Zavialov, R.Gursky, S.Sanyal, M.Ehrenberg, J.Frank, and H.Song (2007).
RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.
  Cell, 129, 929-941.
PDB codes: 2h5e 2o0f
17253975 J.Lacadena, E.Alvarez-García, N.Carreras-Sangrà, E.Herrero-Galán, J.Alegre-Cebollada, L.García-Ortega, M.Oñaderra, J.G.Gavilanes, and A.Martínez del Pozo (2007).
Fungal ribotoxins: molecular dissection of a family of natural killers.
  FEMS Microbiol Rev, 31, 212-237.  
18042701 M.R.Sharma, D.N.Wilson, P.P.Datta, C.Barat, F.Schluenzen, P.Fucini, and R.K.Agrawal (2007).
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
  Proc Natl Acad Sci U S A, 104, 19315-19320.
PDB codes: 3bbn 3bbo
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
17996707 P.P.Datta, D.N.Wilson, M.Kawazoe, N.K.Swami, T.Kaminishi, M.R.Sharma, T.M.Booth, C.Takemoto, P.Fucini, S.Yokoyama, and R.K.Agrawal (2007).
Structural aspects of RbfA action during small ribosomal subunit assembly.
  Mol Cell, 28, 434-445.
PDB codes: 2dyj 2r1c 2r1g
17389639 P.V.Sergiev, A.A.Bogdanov, and O.A.Dontsova (2007).
Ribosomal RNA guanine-(N2)-methyltransferases and their targets.
  Nucleic Acids Res, 35, 2295-2301.  
17179154 R.Gillet, S.Kaur, W.Li, M.Hallier, B.Felden, and J.Frank (2007).
Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
  J Biol Chem, 282, 6356-6363.
PDB code: 2ob7
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.  
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.  
16713583 K.Mitra, C.Schaffitzel, F.Fabiola, M.S.Chapman, N.Ban, and J.Frank (2006).
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
  Mol Cell, 22, 533-543.
PDB codes: 2gy9 2gya 2gyb 2gyc
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.  
16456030 N.Spacková, and J.Sponer (2006).
Molecular dynamics simulations of sarcin-ricin rRNA motif.
  Nucleic Acids Res, 34, 697-708.  
16582919 O.Rackham, K.Wang, and J.W.Chin (2006).
Functional epitopes at the ribosome subunit interface.
  Nat Chem Biol, 2, 254-258.  
17056712 S.Kaur, R.Gillet, W.Li, R.Gursky, and J.Frank (2006).
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
  Proc Natl Acad Sci U S A, 103, 16484-16489.  
16053518 A.Liiv, D.Karitkina, U.Maiväli, and J.Remme (2005).
Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis.
  BMC Mol Biol, 6, 18.  
15876367 A.R.Cukras, and R.Green (2005).
Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation.
  J Mol Biol, 349, 47-59.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
15722438 F.Rázga, J.Koca, J.Sponer, and N.B.Leontis (2005).
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.
  Biophys J, 88, 3466-3485.  
15766541 H.Gao, and J.Frank (2005).
Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement.
  Structure, 13, 401-406.  
16014419 H.Gao, M.J.Ayub, M.J.Levin, and J.Frank (2005).
The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components.
  Proc Natl Acad Sci U S A, 102, 10206-10211.  
  18074004 J.D.Dinman (2005).
5S rRNA: Structure and Function from Head to Toe.
  Int J Biomed Sci, 1, 2-7.  
15601687 K.Lipkow, S.S.Andrews, and D.Bray (2005).
Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli.
  J Bacteriol, 187, 45-53.  
16292303 K.Mitra, C.Schaffitzel, T.Shaikh, F.Tama, S.Jenni, C.L.Brooks, N.Ban, and J.Frank (2005).
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
  Nature, 438, 318-324.
PDB codes: 2akh 2aki
15905403 L.Cochella, and R.Green (2005).
An active role for tRNA in decoding beyond codon:anticodon pairing.
  Science, 308, 1178-1180.  
16120833 M.Sumita, J.P.Desaulniers, Y.C.Chang, H.M.Chui, L.Clos, and C.S.Chow (2005).
Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA.
  RNA, 11, 1420-1429.  
15949441 N.Gao, A.V.Zavialov, W.Li, J.Sengupta, M.Valle, R.P.Gursky, M.Ehrenberg, and J.Frank (2005).
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
  Mol Cell, 18, 663-674.
PDB codes: 1zn0 1zn1
15869392 N.V.Hud, and I.D.Vilfan (2005).
Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size.
  Annu Rev Biophys Biomol Struct, 34, 295-318.  
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
16203986 R.J.Gilbert, L.Beales, D.Blond, M.N.Simon, B.Y.Lin, F.V.Chisari, D.I.Stuart, and D.J.Rowlands (2005).
Hepatitis B small surface antigen particles are octahedral.
  Proc Natl Acad Sci U S A, 102, 14783-14788.  
15117262 C.A.Angell (2004).
Amorphous water.
  Annu Rev Phys Chem, 55, 559-583.  
15315759 C.M.Spahn, E.Jan, A.Mulder, R.A.Grassucci, P.Sarnow, and J.Frank (2004).
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
  Cell, 118, 465-475.  
14976550 C.M.Spahn, M.G.Gomez-Lorenzo, R.A.Grassucci, R.Jørgensen, G.R.Andersen, R.Beckmann, P.A.Penczek, J.P.Ballesta, and J.Frank (2004).
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
  EMBO J, 23, 1008-1019.
PDB codes: 1s1h 1s1i
15627376 I.I.Serysheva (2004).
Structural insights into excitation-contraction coupling by electron cryomicroscopy.
  Biochemistry (Mosc), 69, 1226-1232.  
15334071 J.Sengupta, J.Nilsson, R.Gursky, C.M.Spahn, P.Nissen, and J.Frank (2004).
Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM.
  Nat Struct Mol Biol, 11, 957-962.
PDB code: 1trj
15306816 Q.X.Jiang, D.N.Wang, and R.MacKinnon (2004).
Electron microscopic analysis of KvAP voltage-dependent K+ channels in an open conformation.
  Nature, 430, 806-810.  
15178758 R.K.Agrawal, M.R.Sharma, M.C.Kiel, G.Hirokawa, T.M.Booth, C.M.Spahn, R.A.Grassucci, A.Kaji, and J.Frank (2004).
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
  Proc Natl Acad Sci U S A, 101, 8900-8905.
PDB codes: 1t1m 1t1o
15139808 S.Subramaniam, and J.L.Milne (2004).
Three-dimensional electron microscopy at molecular resolution.
  Annu Rev Biophys Biomol Struct, 33, 141-155.  
15037769 U.Maiväli, and J.Remme (2004).
Definition of bases in 23S rRNA essential for ribosomal subunit association.
  RNA, 10, 600-604.  
15536902 W.V.Nicholson (2004).
Object detection by correlation coefficients using azimuthally averaged reference projections.
  IEEE Trans Biomed Eng, 51, 2006-2012.  
14731293 W.V.Nicholson, and R.Malladi (2004).
Correlation-based methods of automatic particle detection in electron microscopy images with smoothing by anisotropic diffusion.
  J Microsc, 213, 119-128.  
12514741 A.Nikulin, I.Eliseikina, S.Tishchenko, N.Nevskaya, N.Davydova, O.Platonova, W.Piendl, M.Selmer, A.Liljas, D.Drygin, R.Zimmermann, M.Garber, and S.Nikonov (2003).
Structure of the L1 protuberance in the ribosome.
  Nat Struct Biol, 10, 104-108.
PDB code: 1mzp
12859902 A.V.Zavialov, and M.Ehrenberg (2003).
Peptidyl-tRNA regulates the GTPase activity of translation factors.
  Cell, 114, 113-122.  
12878726 F.Tama, M.Valle, J.Frank, and C.L.Brooks (2003).
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.
  Proc Natl Acad Sci U S A, 100, 9319-9323.  
12809609 H.Gao, J.Sengupta, M.Valle, A.Korostelev, N.Eswar, S.M.Stagg, P.Van Roey, R.K.Agrawal, S.C.Harvey, A.Sali, M.S.Chapman, and J.Frank (2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
  Cell, 113, 789-801.
PDB codes: 1p6g 1p85 1p86 1p87
14561879 I.S.Gabashvili, M.Whirl-Carrillo, M.Bada, D.R.Banatao, and R.B.Altman (2003).
Ribosomal dynamics inferred from variations in experimental measurements.
  RNA, 9, 1301-1307.  
14659007 J.Frank (2003).
Toward an understanding of the structural basis of translation.
  Genome Biol, 4, 237.  
12548625 J.Frank (2003).
Electron microscopy of functional ribosome complexes.
  Biopolymers, 68, 223-233.  
14532006 M.R.Sharma, E.C.Koc, P.P.Datta, T.M.Booth, L.L.Spremulli, and R.K.Agrawal (2003).
Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins.
  Cell, 115, 97.  
12859903 M.Valle, A.Zavialov, J.Sengupta, U.Rawat, M.Ehrenberg, and J.Frank (2003).
Locking and unlocking of ribosomal motions.
  Cell, 114, 123-134.
PDB codes: 1pn6 1pn7 1pn8
12574130 S.R.Connell, C.A.Trieber, G.P.Dinos, E.Einfeldt, D.E.Taylor, and K.H.Nierhaus (2003).
Mechanism of Tet(O)-mediated tetracycline resistance.
  EMBO J, 22, 945-953.  
12511960 U.B.Rawat, A.V.Zavialov, J.Sengupta, M.Valle, R.A.Grassucci, J.Linde, B.Vestergaard, M.Ehrenberg, and J.Frank (2003).
A cryo-electron microscopic study of ribosome-bound termination factor RF2.
  Nature, 421, 87-90.
PDB codes: 1mi6 1mvr
12244297 C.S.Tung, S.Joseph, and K.Y.Sanbonmatsu (2002).
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
  Nat Struct Biol, 9, 750-755.
PDB code: 1m5g
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.  
12034847 G.Caetano-Anollés (2002).
Tracing the evolution of RNA structure in ribosomes.
  Nucleic Acids Res, 30, 2575-2587.  
12138121 G.Hirokawa, M.C.Kiel, A.Muto, G.Kawai, K.Igarashi, H.Kaji, and A.Kaji (2002).
Binding of ribosome recycling factor to ribosomes, comparison with tRNA.
  J Biol Chem, 277, 35847-35852.  
12379845 H.Stark, M.V.Rodnina, H.J.Wieden, F.Zemlin, W.Wintermeyer, and M.van Heel (2002).
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
  Nat Struct Biol, 9, 849-854.
PDB code: 1mj1
12007402 J.A.Doudna, and V.L.Rath (2002).
Structure and function of the eukaryotic ribosome: the next frontier.
  Cell, 109, 153-156.  
11756679 J.Brink, S.J.Ludtke, C.Y.Yang, Z.W.Gu, S.J.Wakil, and W.Chiu (2002).
Quaternary structure of human fatty acid synthase by electron cryomicroscopy.
  Proc Natl Acad Sci U S A, 99, 138-143.  
11988472 J.Frank (2002).
Single-particle imaging of macromolecules by cryo-electron microscopy.
  Annu Rev Biophys Biomol Struct, 31, 303-319.  
12176389 J.L.Craighead, W.H.Chang, and F.J.Asturias (2002).
Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA.
  Structure, 10, 1117-1125.  
11867615 M.A.Schäfer, A.O.Tastan, S.Patzke, G.Blaha, C.M.Spahn, D.N.Wilson, and K.H.Nierhaus (2002).
Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit.
  J Biol Chem, 277, 19095-19105.  
12093756 M.Valle, J.Sengupta, N.K.Swami, R.A.Grassucci, N.Burkhardt, K.H.Nierhaus, R.K.Agrawal, and J.Frank (2002).
Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.
  EMBO J, 21, 3557-3567.
PDB codes: 1ls2 1lu3
12198134 T.Uchiumi, S.Honma, Y.Endo, and A.Hachimori (2002).
Ribosomal proteins at the stalk region modulate functional rRNA structures in the GTPase center.
  J Biol Chem, 277, 41401-41409.  
11959506 W.Chiu, M.L.Baker, W.Jiang, and Z.H.Zhou (2002).
Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches.
  Curr Opin Struct Biol, 12, 263-269.  
11738593 A.Roll-Mecak, B.S.Shin, T.E.Dever, and S.K.Burley (2001).
Engaging the ribosome: universal IFs of translation.
  Trends Biochem Sci, 26, 705-709.  
11595494 B.F.McEwen, and J.Frank (2001).
Electron tomographic and other approaches for imaging molecular machines.
  Curr Opin Neurobiol, 11, 594-600.  
11389850 C.M.Spahn, G.Blaha, R.K.Agrawal, P.Penczek, R.A.Grassucci, C.A.Trieber, S.R.Connell, D.E.Taylor, K.H.Nierhaus, and J.Frank (2001).
Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance.
  Mol Cell, 7, 1037-1045.  
11239155 C.M.Spahn, J.S.Kieft, R.A.Grassucci, P.A.Penczek, K.Zhou, J.A.Doudna, and J.Frank (2001).
Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.
  Science, 291, 1959-1962.  
11701127 C.M.Spahn, R.Beckmann, N.Eswar, P.A.Penczek, A.Sali, G.Blobel, and J.Frank (2001).
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
  Cell, 107, 373-386.
PDB codes: 1k5x 1k5y
11149934 E.Nogales, and N.Grigorieff (2001).
Molecular Machines: putting the pieces together.
  J Cell Biol, 152, F1-10.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
12762008 H.F.Noller, M.M.Yusupov, G.Z.Yusupova, A.Baucom, K.Lieberman, L.Lancaster, A.Dallas, K.Fredrick, T.N.Earnest, and J.H.Cate (2001).
Structure of the ribosome at 5.5 A resolution and its interactions with functional ligands.
  Cold Spring Harb Symp Quant Biol, 66, 57-66.  
11511371 I.S.Gabashvili, S.T.Gregory, M.Valle, R.Grassucci, M.Worbs, M.C.Wahl, A.E.Dahlberg, and J.Frank (2001).
The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.
  Mol Cell, 8, 181-188.  
11494321 J.Frank (2001).
Cryo-electron microscopy as an investigative tool: the ribosome as an example.
  Bioessays, 23, 725-732.  
12762009 J.Frank, and R.K.Agrawal (2001).
Ratchet-like movements between the two ribosomal subunits: their implications in elongation factor recognition and tRNA translocation.
  Cold Spring Harb Symp Quant Biol, 66, 67-75.  
11390993 J.Miao, K.O.Hodgson, and D.Sayre (2001).
An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images.
  Proc Natl Acad Sci U S A, 98, 6641-6645.  
11402057 J.R.McIntosh (2001).
Electron microscopy of cells: a new beginning for a new century.
  J Cell Biol, 153, F25-F32.  
11593008 J.Sengupta, R.K.Agrawal, and J.Frank (2001).
Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA.
  Proc Natl Acad Sci U S A, 98, 11991-11996.  
11497427 J.Thompson, W.E.Tapprich, C.Munger, and A.E.Dahlberg (2001).
Staphylococcus aureus domain V functions in Escherichia coli ribosomes provided a conserved interaction with domain IV is restored.
  RNA, 7, 1076-1083.  
11166571 M.V.Rodnina, and W.Wintermeyer (2001).
Ribosome fidelity: tRNA discrimination, proofreading and induced fit.
  Trends Biochem Sci, 26, 124-130.  
11734630 N.V.Hud, and K.H.Downing (2001).
Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids.
  Proc Natl Acad Sci U S A, 98, 14925-14930.  
12762011 P.Sergiev, A.Leonov, S.Dokudovskaya, O.Shpanchenko, O.Dontsova, A.Bogdanov, J.Rinke-Appel, F.Mueller, M.Osswald, K.von Knoblauch, and R.Brimacombe (2001).
Correlating the X-ray structures for halo- and thermophilic ribosomal subunits with biochemical data for the Escherichia coli ribosome.
  Cold Spring Harb Symp Quant Biol, 66, 87.  
12762056 R.Beckmann, C.M.Spahn, J.Frank, and G.Blobel (2001).
The active 80S ribosome-Sec61 complex.
  Cold Spring Harb Symp Quant Biol, 66, 543-554.  
11701126 R.Beckmann, C.M.Spahn, N.Eswar, J.Helmers, P.A.Penczek, A.Sali, J.Frank, and G.Blobel (2001).
Architecture of the protein-conducting channel associated with the translating 80S ribosome.
  Cell, 107, 361-372.  
11600354 S.K.Wilcox, G.S.Cavey, and J.D.Pearson (2001).
Single ribosomal protein mutations in antibiotic-resistant bacteria analyzed by mass spectrometry.
  Antimicrob Agents Chemother, 45, 3046-3055.  
  11780625 V.Ivanov, A.Beniaminov, A.Mikheyev, and E.Minyat (2001).
A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.
  RNA, 7, 1683-1692.  
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
10745014 C.Davies, and S.W.White (2000).
Electrons and X-rays gang up on the ribosome.
  Structure, 8, R41-R45.  
10986461 C.M.Spahn, P.A.Penczek, A.Leith, and J.Frank (2000).
A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.
  Structure, 8, 937-948.  
10998624 E.J.Mancini, and S.D.Fuller (2000).
Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus.
  Acta Crystallogr D Biol Crystallogr, 56, 1278-1287.  
10835368 M.G.Gomez-Lorenzo, C.M.Spahn, R.K.Agrawal, R.A.Grassucci, P.Penczek, K.Chakraburtty, J.P.Ballesta, J.L.Lavandera, J.F.Garcia-Bustos, and J.Frank (2000).
Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolution.
  EMBO J, 19, 2710-2718.  
11258477 M.W.Hentze, E.Izaurralde, and B.Séraphin (2000).
A new era for the RNA world. Conference: RNA 2000.
  EMBO Rep, 1, 394-398.  
10998623 N.Grigorieff (2000).
Resolution measurement in structures derived from single particles.
  Acta Crystallogr D Biol Crystallogr, 56, 1270-1277.  
11080632 R.Brimacombe (2000).
The bacterial ribosome at atomic resolution.
  Structure, 8, R195-R200.  
10931859 R.K.Agrawal, C.M.Spahn, P.Penczek, R.A.Grassucci, K.H.Nierhaus, and J.Frank (2000).
Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle.
  J Cell Biol, 150, 447-460.
PDB code: 1fcw
10969026 W.Wriggers, R.K.Agrawal, D.L.Drew, A.McCammon, and J.Frank (2000).
Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
  Biophys J, 79, 1670-1678.  
11042462 Y.Tao, and W.Zhang (2000).
Recent developments in cryo-electron microscopy reconstruction of single particles.
  Curr Opin Struct Biol, 10, 616-622.  
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.