6QMN | pdb_00006qmn

Crystal structure of a Ribonuclease A-Onconase chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.294 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera.

Esposito, L.Donnarumma, F.Ruggiero, A.Leone, S.Vitagliano, L.Picone, D.

(2019) Int J Biol Macromol 133: 1125-1133

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.04.164
  • Primary Citation Related Structures: 
    6QMN

  • PubMed Abstract: 

    Structural roles of loop regions are frequently overlooked in proteins. Nevertheless, they may be key players in the definition of protein topology and in the self-assembly processes occurring through domain swapping. We here investigate the effects on structure and stability of replacing the loop connecting the last two β-strands of RNase A with the corresponding region of the more thermostable Onconase. The crystal structure of this chimeric variant (RNaseA-ONC) shows that its terminal loop size better adheres to the topological rules for the design of stabilized proteins, proposed by Baker and coworkers [43]. Indeed, RNaseA-ONC displays a thermal stability close to that of RNase A, despite the lack of Pro at position 114, which, due to its propensity to favor a cis peptide bond, has been identified as an important stabilizing factor of the native protein. Accordingly, RNaseA-ONC is significantly more stable than RNase A variants lacking Pro114; RNaseA-ONC also displays a higher propensity to form oligomers in native conditions when compared to either RNase A or Onconase. This finding demonstrates that modifications of terminal loops should to be carefully controlled in terms of size and sequence to avoid unwanted and/or potentially harmful aggregation processes.


  • Organizational Affiliation
    • CNR Istituto di Biostrutture e Bioimmagini, Via Mezzocannone 16, I-80134 Napoli, Italy. Electronic address: luciana.esposito@cnr.it.

Macromolecule Content 

  • Total Structure Weight: 40.76 kDa 
  • Atom Count: 3,003 
  • Modeled Residue Count: 366 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic
A, B, C
122Bison bisonMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61824 (Bison bison)
Explore P61824 
Go to UniProtKB:  P61824
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61824
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.294 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.442α = 90
b = 51.796β = 93.01
c = 66.093γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary