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Ribosomes in the EMDB

7 October 2009: This morning, the recipients of the 2009 Nobel Prize for Chemistry were announced. V. Ramakrishnan, T. A. Steitz, and A. E. Yonath will share the award for their studies on the structure and function of the ribosome. Ribosomes are one of the most frequently studied nucleic acid-protein complexes in electron microscopy. EMDB contains at least 56 ribosome-related entries.


Ribosomes and ribosome-related structures in the EMDB


1003 2002-06-26 RELEASED ON 2002-08-22 singleParticle 11.5Å
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
Gabashvili IS, Agrawal RK, Spahn CM, Grassucci RA, Svergun DI, Frank J, Penczek P
Cell 100(5), 537-49 (2000 Mar 3)

1004 2002-08-27 RELEASED ON 2003-08-29 singleParticle 13Å
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Stark H, Rodnina MV, Wieden HJ, Zemlin F, Wintermeyer W, van Heel M
Nat Struct Biol 9(11), 849-54 (2002 Nov)

1006..1010 2002-09-01 RELEASED ON 2003-09-26 singleParticle 11.3Å
A cryo-electron microscopic study of ribosome-bound termination factor RF2.
Rawat UB, Zavialov AV, Sengupta J, Valle M, Grassucci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J
Nature 421(6918), 87-90 (2003 Jan 2)

1056 2003-09-22 RELEASED ON 2004-01-06 singleParticle 9Å
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
Valle M, Zavialov A, Li W, Stagg SM, Sengupta J, Nielsen RC, Nissen P, Harvey SC, Ehrenberg M, Frank J
Nat Struct Biol 10(11), 899-906 (2003 Nov)

1063 2003-12-19 RELEASED ON 2004-12-19 singleParticle 12.0Å
Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Halic M, Becker T, Pool MR, Spahn CM, Grassucci RA, Frank J, Beckmann R
Nature 427(6977), 808-14 (2004 Feb 26)

1064..1065 2003-12-19 RELEASED ON 2004-12-22 singleParticle 17.9Å
Visualization of release factor 3 on the ribosome during termination of protein synthesis.
Klaholz BP, Myasnikov AG, Van Heel M
Nature 427(6977), 862-5 (2004 Feb 26)

1067 2004-01-05 RELEASED ON 2005-01-06 singleParticle 11.7Å
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jørgensen R, Andersen GR, Beckmann R, Penczek PA, Ballesta JP, Frank J
EMBO J 23(5), 1008-19 (2004 Mar 10)

1068 2004-03-02 RELEASED ON 2004-04-28 singleParticle 13.4Å
Three-dimensional structures of translating ribosomes by Cryo-EM.
Gilbert RJ, Fucini P, Connell S, Fuller SD, Nierhaus KH, Robinson CV, Dobson CM, Stuart DI
Mol Cell 14(1), 57-66 (2004 Apr 9)

1070..1073 2004-03-14 RELEASED ON 2004-04-28 singleParticle 13.4Å
Three-dimensional structures of translating ribosomes by Cryo-EM.
Gilbert RJ, Fucini P, Connell S, Fuller SD, Nierhaus KH, Robinson CV, Dobson CM, Stuart DI
Mol Cell 14(1), 57-66 (2004 Apr 9)

1076 2004-03-10 RELEASED ON 2004-04-07 singleParticle 15.4Å
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J
Cell 107(3), 373-86 (2001 Nov 2)

1077 2004-04-14 RELEASED ON 2005-04-14 singleParticle 12Å
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
Agrawal RK, Sharma MR, Kiel MC, Hirokawa G, Booth TM, Spahn CM, Grassucci RA, Kaji A, Frank J
Proc Natl Acad Sci U S A 101(24), 8900-5 (2004 Jun 15)

1090..1093 2004-08-10 RELEASED ON 2004-11-10 singleParticle 20.3Å
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
Spahn CM, Jan E, Mulder A, Grassucci RA, Sarnow P, Frank J
Cell 118(4), 465-75 (2004 Aug 20)

1110 2005-02-22 RELEASED ON 2005-07-05 singleParticle 18Å
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
Diaconu M, Kothe U, Schlünzen F, Fischer N, Harms JM, Tonevitsky AG, Stark H, Rodnina MV, Wahl MC
Cell 121(7), 991-1004 (2005 Jul 1)

1122 2005-03-24 RELEASED ON 2005-04-11 singleParticle 13Å
Visualizing tmRNA entry into a stalled ribosome.
Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J
Science 300(5616), 127-30 (2003 Apr 4)

1125 2005-02-07 RELEASED ON 2007-05-02 singleParticle 9.5Å
Localization and dynamic behavior of ribosomal protein L30e.
Halic M, Becker T, Frank J, Spahn CM, Beckmann R
Nat Struct Mol Biol 12(5), 467-8 (2005 May)

1138 2005-07-27 RELEASED ON 2006-07-27 singleParticle 15Å
Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.
Boehringer D, Thermann R, Ostareck-Lederer A, Lewis JD, Stark H
Structure 13(11), 1695-706 (2005 Nov)

1143 2005-08-03 RELEASED ON 2006-06-13 singleParticle 14.9Å
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J
Nature 438(7066), 318-24 (2005 Nov 17)

1168..1169 2005-10-10 RELEASED ON 2006-10-10 singleParticle
ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane.
Blau M, Mullapudi S, Becker T, Dudek J, Zimmermann R, Penczek PA, Beckmann R
Nat Struct Mol Biol 12(11), 1015-6 (2005 Nov)

1172..1173 2005-09-14 RELEASED ON 2006-10-27 singleParticle 11.5Å
Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome.
Myasnikov AG, Marzi S, Simonetti A, Giuliodori AM, Gualerzi CO, Yusupova G, Yusupov M, Klaholz BP
Nat Struct Mol Biol 12(12), 1145-9 (2005 Dec)

1184..1185 2006-01-31 RELEASED ON 2006-05-09 singleParticle 12.8Å
Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM.
Rawat U, Gao H, Zavialov A, Gursky R, Ehrenberg M, Frank J
J Mol Biol 357(4), 1144-53 (2006 Apr 7)

1197..1199 2006-02-28 RELEASED ON 2006-05-11 singleParticle 16.2Å
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting.
Namy O, Moran SJ, Stuart DI, Gilbert RJ, Brierley I
Nature 441(7090), 244-7 (2006 May 11)

1211..1212 2006-03-28 RELEASED ON 2006-06-01 singleParticle 34Å
Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit.
Schäfer T, Maco B, Petfalski E, Tollervey D, Böttcher B, Aebi U, Hurt E
Nature 441(7093), 651-5 (2006 Jun 1)

1233 2006-06-27 RELEASED ON 2006-10-12 singleParticle 9.9Å
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
Andersen CB, Becker T, Blau M, Anand M, Halic M, Balar B, Mielke T, Boesen T, Pedersen JS, Spahn CM, Kinzy TG, Andersen GR, Beckmann R
Nature 443(7112), 663-8 (2006 Oct 12)

1250..1251 2006-07-28 RELEASED ON 2008-07-29 singleParticle 15.5Å
Structure of the E. coli signal recognition particle bound to a translating ribosome.
Schaffitzel C, Oswald M, Berger I, Ishikawa T, Abrahams JP, Koerten HK, Koning RI, Ban N
Nature 444(7118), 503-6 (2006 Nov 23)

1261..1264 2006-08-21 RELEASED ON 2007-08-28 singleParticle 9.5Å
Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
Halic M, Blau M, Becker T, Mielke T, Pool MR, Wild K, Sinning I, Beckmann R
Nature 444(7118), 507-11 (2006 Nov 23)

1285 2006-10-31 RELEASED ON 2007-10-31 singleParticle 7.3Å
Structure of the ribosome-bound cricket paralysis virus IRES RNA.
Schüler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM
Nat Struct Mol Biol 13(12), 1092-6 (2006 Dec)

1302 2006-11-29 RELEASED ON 2007-06-22 singleParticle 15.5Å
RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.
Gao H, Zhou Z, Rawat U, Huang C, Bouakaz L, Wang C, Cheng Z, Liu Y, Zavialov A, Gursky R, Sanyal S, Ehrenberg M, Frank J, Song H
Cell 129(5), 929-41 (2007 Jun 1)

1303 2006-12-01 RELEASED ON 2006-12-01 singleParticle 12Å
The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components.
Gao H, Ayub MJ, Levin MJ, Frank J
Proc Natl Acad Sci U S A 102(29), 10206-11 (2005 Jul 19)

1310 2006-12-12 RELEASED ON 2007-06-12 singleParticle 11.8Å
Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Gillet R, Kaur S, Li W, Hallier M, Felden B, Frank J
J Biol Chem 282(9), 6356-63 (2007 Mar 2)

1311 2006-12-13 RELEASED ON 2006-12-14 singleParticle 13.6Å
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.
Kaur S, Gillet R, Li W, Gursky R, Frank J
Proc Natl Acad Sci U S A 103(44), 16484-9 (2006 Oct 31)

1312 2006-12-13 RELEASED ON 2007-12-14 singleParticle 13.1Å
Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Gillet R, Kaur S, Li W, Hallier M, Felden B, Frank J
J Biol Chem 282(9), 6356-63 (2007 Mar 2)

1315 2007-01-18 RELEASED ON 2008-01-19 singleParticle 7.3Å
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Connell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schüler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM
Mol Cell 25(5), 751-64 (2007 Mar 9)

1323..1324 2007-02-15 RELEASED ON 2007-04-18 singleParticle 16Å
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
Konevega AL, Fischer N, Semenkov YP, Stark H, Wintermeyer W, Rodnina MV
Nat Struct Mol Biol 14(4), 318-24 (2007 Apr)

1342..1345 2007-03-20 RELEASED ON 2007-06-12 singleParticle 11.3Å
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
Taylor DJ, Nilsson J, Merrill AR, Andersen GR, Nissen P, Frank J
EMBO J 26(9), 2421-31 (2007 May 2)

1346..1349 2007-03-27 RELEASED ON 2007-06-06 singleParticle 21Å
The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome.
Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, Algire MA, Lorsch JR, Ramakrishnan V
Mol Cell 26(1), 41-50 (2007 Apr 13)

1362..1366 2007-05-18 RELEASED ON 2007-05-24 singleParticle 12.5Å
Locking and unlocking of ribosomal motions.
Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J
Cell 114(1), 123-34 (2003 Jul 11)

1369..1370 2007-06-01 RELEASED ON 2008-01-07 singleParticle 18.4Å
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
Barat C, Datta PP, Raj VS, Sharma MR, Kaji H, Kaji A, Agrawal RK
Mol Cell 27(2), 250-61 (2007 Jul 20)

1391 2007-06-22 RELEASED ON 2007-11-15 singleParticle 10Å
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
Marzi S, Myasnikov AG, Serganov A, Ehresmann C, Romby P, Yusupov M, Klaholz BP
Cell 130(6), 1019-31 (2007 Sep 21)

1395 2007-07-27 RELEASED ON 2007-08-02 singleParticle 12.8Å
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
Valle M, Zavialov A, Li W, Stagg SM, Sengupta J, Nielsen RC, Nissen P, Harvey SC, Ehrenberg M, Frank J
Nat Struct Biol 10(11), 899-906 (2003 Nov)

1417 2007-08-31 ON HOLD singleParticle 9.4Å
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
Sharma MR, Wilson DN, Datta PP, Barat C, Schluenzen F, Fucini P, Agrawal RK
Proc Natl Acad Sci U S A 104(49), 19315-20 (2007 Dec 4)

1430 2007-09-24 RELEASED ON 2007-12-12 singleParticle 9.1Å
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
Gao N, Zavialov AV, Ehrenberg M, Frank J
J Mol Biol 374(5), 1345-58 (2007 Dec 14)

1480 2008-02-24 RELEASED ON 2009-03-31 singleParticle 8.7Å
Structure of the mammalian 80S ribosome at 8.7 A resolution.
Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW
Structure 16(4), 535-48 (2008 Apr)

1484 2008-02-26 RELEASED ON 2009-05-29 singleParticle 9.6Å
Ribosome binding of a single copy of the SecY complex: implications for protein translocation.
Ménétret JF, Schaletzky J, Clemons WM, Osborne AR, Skånland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW
Mol Cell 28(6), 1083-92 (2007 Dec 28)

1499 2008-04-04 RELEASED ON 2009-05-29 singleParticle 19Å
Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
Merz F, Boehringer D, Schaffitzel C, Preissler S, Hoffmann A, Maier T, Rutkowska A, Lozza J, Ban N, Bukau B, Deuerling E
EMBO J 27(11), 1622-32 (2008 Jun 4)

1524 2008-06-10 RELEASED ON 2009-04-01 singleParticle 10.9Å
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
Connell SR, Topf M, Qin Y, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CM
Nat Struct Mol Biol 15(9), 910-5 (2008 Sep)

1528 2008-06-23 RELEASED ON 2009-04-15 singleParticle 8.7Å
Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.
Ménétret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW
Structure 16(7), 1126-37 (2008 Jul)

1540..1541 2008-08-12 RELEASED ON 2009-08-26 singleParticle 10.5Å
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
Agirrezabala X, Lei J, Brunelle JL, Ortiz-Meoz RF, Green R, Frank J
Mol Cell 32(2), 190-7 (2008 Oct 24)

1551,1553..1554 2008-09-08 RELEASED ON 2009-05-05 singleParticle 13Å
Structure of ratcheted ribosomes with tRNAs in hybrid states.
Julián P, Konevega AL, Scheres SH, Lázaro M, Gil D, Wintermeyer W, Rodnina MV, Valle M
Proc Natl Acad Sci U S A 105(44), 16924-7 (2008 Nov 4)

1564..1565 2008-09-29 ON HOLD singleParticle 12Å
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
Li W, Agirrezabala X, Lei J, Bouakaz L, Brunelle JL, Ortiz-Meoz RF, Green R, Sanyal S, Ehrenberg M, Frank J
EMBO J 27(24), 3322-31 (2008 Dec 17)

1582 2008-11-07 RELEASED ON 2009-06-11 singleParticle 30Å
The native 3D organization of bacterial polysomes.
Brandt F, Etchells SA, Ortiz JO, Elcock AH, Hartl FU, Baumeister W
Cell 136(2), 261-71 (2009 Jan 23)

1615..1616 2009-04-23 ON HOLD singleParticle 14.4Å
YidC and Oxa1 form dimeric insertion pores on the translating ribosome.
Kohler R, Boehringer D, Greber B, Bingel-Erlenmeyer R, Collinson I, Schaffitzel C, Ban N
Mol Cell 34(3), 344-53 (2009 May 15)

5015..5017 2008-06-20 RELEASED ON 2009-05-05 singleParticle 12.6Å
Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
Sengupta J, Nilsson J, Gursky R, Kjeldgaard M, Nissen P, Frank J
J Mol Biol 382(1), 179-87 (2008 Sep 26)

5030 2008-10-30 RELEASED ON 2009-05-05 singleParticle 6.4Å
GTPase activation of elongation factor EF-Tu by the ribosome during decoding.
Schuette JC, Murphy FV, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CM
EMBO J , (2009 Feb 19)

5036 2008-12-01 RELEASED ON 2009-05-05 singleParticle 6.7Å
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Trabuco LG, Villa E, Mitra K, Frank J, Schulten K
Structure 16(5), 673-83 (2008 May)

5041..5047 2009-01-08 RELEASED ON 2009-09-04 singleParticle 24Å
Survey of large protein complexes in D. vulgaris reveals unexpected structural diversity
Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, Glaeser RM

5113 2009-03-16 RELEASED ON 2009-05-15 singleParticle 14.1Å
Structure of a mitochondrial ribosome with minimal RNA.
Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK
Proc Natl Acad Sci U S A 106(24), 9637-42 (2009 Jun 16)