488D

CATALYTIC RNA ENZYME-PRODUCT COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.

Murray, J.B.Szoke, H.Szoke, A.Scott, W.G.

(2000) Mol Cell 5: 279-287

  • DOI: https://doi.org/10.1016/s1097-2765(00)80423-2
  • Primary Citation of Related Structures:  
    488D

  • PubMed Abstract: 

    We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure. Subsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately perpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe several interactions with functional groups on these residues that have been identified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. These interactions may therefore be relevant to the hammerhead ribozyme reaction mechanism.


  • Organizational Affiliation

    The Center for the Molecular Biology of RNA and Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA RIBOZYME STRAND16N/A
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE20N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE5N/A
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Entity ID: 4
MoleculeChains LengthOrganismImage
UNCLEAVED RNA SUBSTRATE25N/A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.503α = 90
b = 65.503β = 90
c = 136.484γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations