1FFZ

LARGE RIBOSOMAL SUBUNIT COMPLEXED WITH R(CC)-DA-PUROMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structural basis of ribosome activity in peptide bond synthesis.

Nissen, P.Hansen, J.Ban, N.Moore, P.B.Steitz, T.A.

(2000) Science 289: 920-930

  • DOI: 10.1126/science.289.5481.920
  • Primary Citation of Related Structures:  
    1FG0, 1FFZ

  • PubMed Abstract: 
  • Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized ...

    Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.


    Related Citations: 
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
      Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A.
      (2000) Science 289: 905
    • Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit
      Ban, N., Nissen, P., Hansen, J., Capel, M., Moore, P.B., Steitz, T.A.
      (1999) Nature 400: 841
    • An inhibitor of ribosomal peptidyl transferase using transition-state analogy
      Welch, M., Chastang, J., Yarus, M.
      (1995) Biochemistry 34: 385

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.



Macromolecules
Find similar nucleic acids by: Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAA602Haloarcula marismortui
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    R(P*CP*C*)-D(P*A)-R(P*(PU))B4N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 212α = 90
    b = 300β = 90
    c = 574γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSrefinement
    Omodel building
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-08-28
      Type: Initial release
    • Version 1.1: 2008-04-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance