3SNP | pdb_00003snp

Crystal structure analysis of iron regulatory protein 1 in complex with ferritin H IRE RNA

• PDB DOI: https://doi.org/10.2210/pdb3SNP/pdb
• Entry: 3SNP supersedes: 2IPY
• NAKB: 3SNP

• Classification: LYASE/RNA
• Organism(s): Oryctolagus cuniculus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2011-06-29 Released: 2011-07-27 
• Deposition Author(s): Volz, K., Selezneva, A.I., Walden, W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Models: experimental

Literature

Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA.

Walden, W.E., Selezneva, A.I., Dupuy, J., Volbeda, A., Fontecilla-Camps, J.C., Theil, E.C., Volz, K.

(2006) Science 314: 1903-1908

• PubMed: 17185597 
• DOI: https://doi.org/10.1126/science.1133116
• Primary Citation Related Structures: 
  3SNP


• PubMed Abstract: 
  

  Iron regulatory protein 1 (IRP1) binds iron-responsive elements (IREs) in messenger RNAs (mRNAs), to repress translation or degradation, or binds an iron-sulfur cluster, to become a cytosolic aconitase enzyme. The 2.8 angstrom resolution crystal structure of the IRP1:ferritin H IRE complex shows an open protein conformation compared with that of cytosolic aconitase. The extended, L-shaped IRP1 molecule embraces the IRE stem-loop through interactions at two sites separated by approximately 30 angstroms, each involving about a dozen protein:RNA bonds. Extensive conformational changes related to binding the IRE or an iron-sulfur cluster explain the alternate functions of IRP1 as an mRNA regulator or enzyme.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 220.69 kDa 
• Atom Count: 15,113 
• Modeled Residue Count: 1,760 
• Deposited Residue Count: 1,876 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic aconitate hydratase	A, B	908	Oryctolagus cuniculus	Mutation(s): 2  Gene Names: ACO1, FRP, IREB1, IREBP, IRP1 EC: 4.2.1.3
UniProt
Find proteins for Q01059 (Oryctolagus cuniculus) Explore Q01059  Go to UniProtKB:  Q01059

Entity ID: 2
Molecule	Chains	Length	Organism	Image
ferritin H IRE RNA	C, D	30	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.555	α = 90
b = 80.851	β = 92.03
c = 142.873	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Volz, K., Selezneva, A.I., Walden, W.E.
• This entry supersedes: 2IPY

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Advisory
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-13
  Changes: Advisory, Data collection, Database references, Refinement description