1DRZ

U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX

• PDB DOI:  https://doi.org/10.2210/pdb1DRZ/pdb
• NAKB: 1DRZ

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Hepatitis delta virus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-09-01 Released: 1999-02-16 
• Deposition Author(s): Ferre-D'Amare, A.R., Zhou, K., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.281 
• R-Value Observed: 0.281 

Literature

Crystal structure of a hepatitis delta virus ribozyme.

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

(1998) Nature 395: 567-574

• PubMed: 9783582 
• DOI: https://doi.org/10.1038/26912
• Primary Citation of Related Structures:  
  1DRZ


• 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-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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.84 kDa 
• Atom Count: 2,366 
• Modelled Residue Count: 167 
• Deposited Residue Count: 169 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A)	B [auth A]	97	Homo sapiens	Mutation(s): 2  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME)	A [auth B]	72	Hepatitis delta virus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth B], D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.281 
• R-Value Observed: 0.281 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.35	α = 90
b = 109.35	β = 90
c = 190.68	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Ferre-D'Amare, A.R., Zhou, K., Doudna, J.A.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations