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 1.2 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: 10.1016/s1097-2765(00)80423-2
  • Structures With Same Primary Citation

  • 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 el ...

    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
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
RNA RIBOZYME STRANDA16N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
FIRST RNA FRAGMENT OF CLEAVED SUBSTRATEB20N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
SECOND RNA FRAGMENT OF CLEAVED SUBSTRATEC5N/A

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Entity ID: 4
MoleculeChainsLengthOrganism
UNCLEAVED RNA SUBSTRATED25N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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