3LJD

The X-ray structure of zebrafish RNase1 from a new crystal form at pH 4.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.

Pizzo, E.Merlino, A.Turano, M.Russo Krauss, I.Coscia, F.Zanfardino, A.Varcamonti, M.Furia, A.Giancola, C.Mazzarella, L.Sica, F.D'Alessio, G.

(2010) Biochem.J. 433: 345-355

  • DOI: 10.1042/BJ20100892
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, the ...

    Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily.


    Related Citations: 
    • Ribonucleases and angiogenins from fish
      Pizzo, E.,Buonanno, P.,DI Maro, A.,Ponticelli, S.,De Falco, S.,Quarto, N.,Cubellis, M.V.,D'Alessio, G.
      (2006) J.Biol.Chem. 281: 27454


    Organizational Affiliation

    Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zebrafish RNase1
A, B
126Danio rerioMutation(s): 0 
Find proteins for E7FH76 (Danio rerio)
Go to UniProtKB:  E7FH76
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.339α = 90.00
b = 48.971β = 90.00
c = 109.913γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
CNSrefinement
HKL-2000data scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Database references