VENKATRAMAN RAMAKRISHNAN

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi request reprint The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit
    D E Brodersen
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Cell 103:1143-54. 2000
  2. doi request reprint The ribosome: some hard facts about its structure and hot air about its evolution
    V Ramakrishnan
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
    Cold Spring Harb Symp Quant Biol 74:25-33. 2009
  3. pmc Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome
    Rebecca M Voorhees
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 16:528-33. 2009
  4. pmc Unusual base pairing during the decoding of a stop codon by the ribosome
    Israel S Fernández
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Nature 500:107-10. 2013
  5. pmc How mutations in tRNA distant from the anticodon affect the fidelity of decoding
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 18:432-6. 2011
  6. pmc The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome
    Rebecca M Voorhees
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 20:641-3. 2013
  7. pmc The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE
    Cajetan Neubauer
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Cell 139:1084-95. 2009
  8. ncbi request reprint Atomic structures at last: the ribosome in 2000
    V Ramakrishnan
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Curr Opin Struct Biol 11:144-54. 2001
  9. doi request reprint What we have learned from ribosome structures
    V Ramakrishnan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge
    Biochem Soc Trans 36:567-74. 2008
  10. ncbi request reprint Ribosome structure and the mechanism of translation
    V Ramakrishnan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Cell 108:557-72. 2002

Research Grants

  1. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2003
  2. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2004
  3. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2005
  4. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2006

Collaborators

Detail Information

Publications35

  1. ncbi request reprint The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit
    D E Brodersen
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Cell 103:1143-54. 2000
    ..For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function...
  2. doi request reprint The ribosome: some hard facts about its structure and hot air about its evolution
    V Ramakrishnan
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
    Cold Spring Harb Symp Quant Biol 74:25-33. 2009
    ..In addition to facilitating our understanding of ribosome function, these structures also shed light on the evolution of the ribosome...
  3. pmc Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome
    Rebecca M Voorhees
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 16:528-33. 2009
    ..They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer...
  4. pmc Unusual base pairing during the decoding of a stop codon by the ribosome
    Israel S Fernández
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Nature 500:107-10. 2013
    ..The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs. ..
  5. pmc How mutations in tRNA distant from the anticodon affect the fidelity of decoding
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 18:432-6. 2011
    ..Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding...
  6. pmc The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome
    Rebecca M Voorhees
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 20:641-3. 2013
    ..The structure illustrates how agmatidine confers codon specificity for AUA over AUG...
  7. pmc The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE
    Cajetan Neubauer
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Cell 139:1084-95. 2009
    ..These structures provide detailed insight into the translational regulation on the bacterial ribosome by mRNA cleavage...
  8. ncbi request reprint Atomic structures at last: the ribosome in 2000
    V Ramakrishnan
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Curr Opin Struct Biol 11:144-54. 2001
    ..A year before that, a 7.8 A resolution electron density map of the 70S ribosome from T. thermophilus appeared. This information is revolutionizing our understanding of protein synthesis...
  9. doi request reprint What we have learned from ribosome structures
    V Ramakrishnan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge
    Biochem Soc Trans 36:567-74. 2008
    ....
  10. ncbi request reprint Ribosome structure and the mechanism of translation
    V Ramakrishnan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Cell 108:557-72. 2002
    ..This review is an attempt to correlate the structures with biochemical and genetic data to identify the gaps and limits in our current knowledge of the mechanisms involved in translation...
  11. ncbi request reprint The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome
    Lori A Passmore
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK
    Mol Cell 26:41-50. 2007
    ..Our results suggest that eIF1 and eIF1A promote an open, scanning-competent preinitiation complex that closes upon start codon recognition and eIF1 release to stabilize ternary complex binding and clamp down on mRNA...
  12. ncbi request reprint Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA
    Ditlev E Brodersen
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge CB2 2QH, UK
    J Mol Biol 316:725-68. 2002
    ..We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit...
  13. ncbi request reprint Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
    ..The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs...
  14. ncbi request reprint Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
    A P Carter
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nature 407:340-8. 2000
    ..This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process...
  15. ncbi request reprint Structure of the 70S ribosome complexed with mRNA and tRNA
    Maria Selmer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 313:1935-42. 2006
    ..The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation...
  16. doi request reprint What recent ribosome structures have revealed about the mechanism of translation
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Nature 461:1234-42. 2009
    ..In this review, we discuss how the interaction between structural and functional studies over the last decade has led to a deeper understanding of the complex mechanisms underlying translation...
  17. pmc The structure of the ribosome with elongation factor G trapped in the posttranslocational state
    Yong Gui Gao
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
    Science 326:694-9. 2009
    ..The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure...
  18. ncbi request reprint Structural insights into translational fidelity
    James M Ogle
    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
    Annu Rev Biochem 74:129-77. 2005
    ..However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting...
  19. ncbi request reprint Molecular biology. A renewed focus on transfer RNA
    Tina Daviter
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 308:1123-4. 2005
  20. ncbi request reprint Selection of tRNA by the ribosome requires a transition from an open to a closed form
    James M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom
    Cell 111:721-32. 2002
    ..We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity...
  21. ncbi request reprint Crystal structure of an initiation factor bound to the 30S ribosomal subunit
    A P Carter
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 291:498-501. 2001
    ..The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit...
  22. pmc The mechanism for activation of GTP hydrolysis on the ribosome
    Rebecca M Voorhees
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Science 330:835-8. 2010
    ..The structure suggests a universal mechanism for GTPase activation and hydrolysis in translational GTPases on the ribosome...
  23. pmc The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
    Science 326:688-94. 2009
    ..A series of conformational changes in EF-Tu and aminoacyl-tRNA suggests a communication pathway between the decoding center and the guanosine triphosphatase center of EF-Tu...
  24. pmc Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release
    Hong Jin
    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Proc Natl Acad Sci U S A 107:8593-8. 2010
    ....
  25. doi request reprint The termination of translation
    Sabine Petry
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
    Curr Opin Struct Biol 18:70-7. 2008
    ..However, a detailed understanding of the underlying mechanisms will require higher-resolution structures of the various states involved...
  26. ncbi request reprint Crystal structure of the ribosome recycling factor bound to the ribosome
    Albert Weixlbaumer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nat Struct Mol Biol 14:733-7. 2007
    ..This suggests that such changes are not a direct requirement for or consequence of RRF binding but possibly arise from the subsequent stabilization of a hybrid state of the ribosome...
  27. ncbi request reprint Structure of the 30S ribosomal subunit
    B T Wimberly
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nature 407:327-39. 2000
    ..The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography...
  28. ncbi request reprint Insights into the decoding mechanism from recent ribosome structures
    James M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Trends Biochem Sci 28:259-66. 2003
    ..In conjunction with recent cryoelectron microscopy structures of the ribosome, a comprehensive structural understanding of the decoding process is beginning to emerge...
  29. ncbi request reprint Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination
    W M Clemons
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 310:827-43. 2001
    ....
  30. pmc Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3
    C Leong Ng
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 17:1241-6. 2010
    ..These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function...
  31. pmc Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit
    Christine M Dunham
    MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
    RNA 13:817-23. 2007
    ..Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center...
  32. ncbi request reprint Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon
    Sabine Petry
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Cell 123:1255-66. 2005
    ..Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway...
  33. pmc Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines
    Albert Weixlbaumer
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Struct Mol Biol 14:498-502. 2007
    ..U base pair in standard Watson-Crick geometry, which presumably involves an enol form for the uridine. These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA...
  34. ncbi request reprint Phasing the 30S ribosomal subunit structure
    D E Brodersen
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
    Acta Crystallogr D Biol Crystallogr 59:2044-50. 2003
    ..In addition, measures to counter problems with non-isomorphism and radiation decay are described...
  35. ncbi request reprint Structure of a purine-purine wobble base pair in the decoding center of the ribosome
    Frank V Murphy
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Struct Mol Biol 11:1251-2. 2004
    ..A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position...

Research Grants4

  1. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2003
    ..Such knowledge could help improve existing antibiotics and could also lead to the design of new ones. ..
  2. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2004
    ..Such knowledge could help improve existing antibiotics and could also lead to the design of new ones. ..
  3. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2005
    ..Such knowledge could help improve existing antibiotics and could also lead to the design of new ones. ..
  4. Structural studies on ribosomes and antibiotics
    VENKATRAMAN RAMAKRISHNAN; Fiscal Year: 2006
    ..Such knowledge could help improve existing antibiotics and could also lead to the design of new ones. ..