1DRZ

U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a hepatitis delta virus ribozyme.

Ferre-D'Amare, A.R.Zhou, K.Doudna, J.A.

(1998) Nature 395: 567-574

  • DOI: 10.1038/26912
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X ...

    The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X-rays to 2.3 A resolution by engineering the RNA to bind a small, basic protein without affecting ribozyme activity. The co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. The 5'-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A)
A
97Homo sapiensMutations: H30Y, R35Q
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME)B72Hepatitis delta virus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.281 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 109.350α = 90.00
b = 109.350β = 90.00
c = 190.680γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance