2BEX

Crystal structure of Placental Ribonuclease Inhibitor in complex with Human Eosinophil Derived Neurotoxin at 2A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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This is version 1.2 of the entry. See complete history. 


Literature

Molecular Recognition of Human Eosinophil-Derived Neurotoxin (Rnase 2) by Placental Ribonuclease Inhibitor

Iyer, S., Holloway, D.E., Kumar, K., Shapiro, R., Acharya, K.R.

(2005) J Mol Biol 347: 637

  • DOI: 10.1016/j.jmb.2005.01.035
  • Primary Citation of Related Structures:  
    2BEX

  • PubMed Abstract: 

    • Placental ribonuclease inhibitor (RI) binds diverse mammalian RNases with dissociation constants that are in the femtomolar range. Previous studies on the complexes of RI with RNase A and angiogenin revealed that RI utilises largely distinctive interactions to achieve high affinity for these two ligands ...

    Placental ribonuclease inhibitor (RI) binds diverse mammalian RNases with dissociation constants that are in the femtomolar range. Previous studies on the complexes of RI with RNase A and angiogenin revealed that RI utilises largely distinctive interactions to achieve high affinity for these two ligands. Here we report a 2.0 angstroms resolution crystal structure of RI in complex with a third ligand, eosinophil-derived neurotoxin (EDN), and a mutational analysis based on this structure. The RI-EDN interface is more extensive than those of the other two complexes and contains a considerably larger set of interactions. Few of the contacts present in the RI-angiogenin complex are replicated; the correspondence to the RI-RNase A complex is somewhat greater, but still modest. The energetic contributions of various interface regions differ strikingly from those in the earlier complexes. These findings provide insight into the structural basis for the unusual combination of high avidity and relaxed stringency that RI displays.

    Organizational Affiliation: 

    Department of Biology and Biochemistry, 4 South, University of Bath, Claverton Down, Bath BA2 7AY, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE INHIBITORA, B460Homo sapiensMutation(s): 0 
Gene Names: RNH1, PRI, RNH
UniProt & NIH Common Fund Data Resources
Find proteins for P13489 (Homo sapiens)
Explore P13489 
Go to UniProtKB:  P13489
PHAROS:  P13489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13489
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NONSECRETORY RIBONUCLEASEC, D135Homo sapiensMutation(s): 0 
Gene Names: RNASE2, EDN, RNS2
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P10153 (Homo sapiens)
Explore P10153 
Go to UniProtKB:  P10153
PHAROS:  P10153
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10153
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAK
Query on MAK
Download Ideal Coordinates CCD File 
F [auth B]ALPHA-KETOMALONIC ACID
C3 H2 O5
XEEVLJKYYUVTRC-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.98α = 90
b = 91.98β = 90
c = 257.65γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance