Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.14 kDa 
• Atom Count: 2,380 
• Modelled Residue Count: 169 
• Deposited Residue Count: 176 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 4PRF

A Second Look at the HDV Ribozyme Structure and Dynamics.

• PDB DOI: 10.2210/pdb4PRF/pdb
• Entry: 4PRF supersedes: 1VC7
• NDB: NA2948

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


• Deposited: 2014-03-05 Released: 2014-10-29 
• Deposition Author(s): Kapral, G.J., Jain, S., Noeske, J., Doudna, J.A., Richardson, D.C., Richardson, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.

Kapral, G.J., Jain, S., Noeske, J., Doudna, J.A., Richardson, D.C., Richardson, J.S.

(2014) Nucleic Acids Res 42: 12833-12846

• PubMed: 25326328 
• DOI: 10.1093/nar/gku992
• Primary Citation of Related Structures:  
  4PR6, 4PRF


• PubMed Abstract: 
  

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.

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Organizational Affiliation: 

Department of Biochemistry, Duke University, Durham, NC 27710, USA [e-mail].

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	B [auth A]	100	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
Hepatitis Delta virus ribozyme	A [auth B]	76	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	C [auth B], D [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.944	α = 90
b = 108.944	β = 90
c = 191.754	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Kapral, G.J., Jain, S., Noeske, J., Doudna, J.A., Richardson, D.C., Richardson, J.S.
• This entry supersedes: 1VC7

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references