7BFL

X-ray structure of SS-RNase-2 des116-120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structural features of an ancient ribonuclease from Salmo salar reveal an intriguing case of auto-inhibition.

Sica, F.Russo Krauss, I.Troisi, R.Bosso, A.Culurciello, R.Carluccio, C.Trapani, M.Merlino, A.Mazzarella, L.Pizzo, E.

(2021) Int J Biol Macromol 182: 659-668

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.04.041
  • Primary Citation of Related Structures:  
    7BFK, 7BFL

  • PubMed Abstract: 

    The superfamily of vertebrate ribonucleases, a large group of evolutionarily related proteins, continues to provide interesting structural and functional information. In particular, the crystal structure of SS-RNase-2 from Salmo salar (SS2), here presented, has revealed a novel auto-inhibition mechanism that enriches the number of inhibition strategies observed in some members of the family. Within an essentially unmodified RNase folding, the SS2 active site cleft is in part obstructed by the collapse of an extra pentapeptide inserted in the C-terminal region. This unexpected intrusion alters the organization of the catalytic triad by pushing one catalytic histidine off the pocket. Possible mechanisms to remove the active site obstruction have also been studied through the production of two mutants that provide useful information on the functionality of this intriguing version of the ribonuclease superfamily.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy. Electronic address: filomena.sica@unina.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiogenin-1
A, B, C, D
122Salmo salarMutation(s): 0 
Gene Names: ANG1ang1
UniProt
Find proteins for B5XAZ0 (Salmo salar)
Explore B5XAZ0 
Go to UniProtKB:  B5XAZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5XAZ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.07α = 90
b = 93.07β = 117.19
c = 66.78γ = 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: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary