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 

wwPDB Validation 3D Report Full Report


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

  • 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 inter ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE INHIBITOR
A, B
460Homo sapiensMutation(s): 0 
Gene Names: RNH1 (PRI, RNH)
Find proteins for P13489 (Homo sapiens)
Go to Gene View: RNH1
Go to UniProtKB:  P13489
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NONSECRETORY RIBONUCLEASE
C, D
135Homo sapiensMutation(s): 0 
Gene Names: RNASE2 (EDN, RNS2)
EC: 4.6.1.18
Find proteins for P10153 (Homo sapiens)
Go to Gene View: RNASE2
Go to UniProtKB:  P10153
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAK
Query on MAK

Download SDF File 
Download CCD File 
B
ALPHA-KETOMALONIC ACID
C3 H2 O5
XEEVLJKYYUVTRC-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 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.980α = 90.00
b = 91.980β = 90.00
c = 257.650γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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