6F7T

Crystal Structure of an Fab fragment in complex with a peptide from Bacillus subtilis RNase Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding.

Hardouin, P.Velours, C.Bou-Nader, C.Assrir, N.Laalami, S.Putzer, H.Durand, D.Golinelli-Pimpaneau, B.

(2018) Biophys. J. 115: 2102-2113

  • DOI: 10.1016/j.bpj.2018.10.016

  • PubMed Abstract: 
  • Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b ...

    Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b λx isotype was raised against a 12-residue conserved peptide from the N-terminal noncatalytic domain of B. subtilis RNase Y (BsRNaseY) that is predicted to be intrinsically disordered. Here, we show that this domain can be produced as a stand-alone protein called Nter-BsRNaseY that undergoes conformational changes between monomeric and dimeric forms. Circular dichroism and size exclusion chromatography coupled with multiangle light scattering or with small angle x-ray scattering indicate that the Nter-BsRNaseY dimer displays an elongated form and a high content of α-helices, in agreement with the existence of a central coiled-coil structure appended with flexible ends, and that the monomeric state of Nter-BsRNaseY is favored upon binding the fragment antigen binding (Fab) of the antibody. The dissociation constants of the IgG/BsRNaseY, IgG/Nter-BsRNaseY, and IgG/peptide complexes indicate that the affinity of the IgG for Nter-BsRNaseY is in the nM range and suggest that the peptide is less accessible in BsRNaseY than in Nter-BsRNaseY. The crystal structure of the Fab in complex with the peptide antigen shows that the peptide adopts an elongated U-shaped conformation in which the unique hydrophobic residue of the peptide, Leu6, is completely buried. The peptide/Fab complex may mimic the interaction of a microdomain of the N-terminal domain of BsRNaseY with one of its cellular partners within the degradosome complex. Altogether, our results suggest that BsRNaseY may become accessible for protein interaction upon dissociation of its N-terminal domain into the monomeric form.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France.,Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France. Electronic address: beatrice.golinelli@college-de-france.fr.,Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France.,CNRS UMR8261-Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB RY79-90, LIGHT CHAIN
A, L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB RY79-90, HEAVY CHAIN
B, H
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease Y
C, D
12Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rny (ymdA)
EC: 3.1.-.-
Find proteins for O31774 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31774
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.680α = 90.00
b = 130.450β = 90.00
c = 72.050γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LABEX DynamoFranceANR-11-LABX-0011
French National Research AgencyFranceANR-11-BSV8-026

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-28
    Type: Data collection, Database references
  • Version 1.2: 2018-12-19
    Type: Data collection, Database references