5OAB

A novel crystal form of human RNase6 at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates.

Prats-Ejarque, G.Blanco, J.A.Salazar, V.A.Nogues, V.M.Moussaoui, M.Boix, E.

(2019) Biochim Biophys Acta Gen Subj 1863: 105-117

  • DOI: 10.1016/j.bbagen.2018.09.021
  • Primary Citation of Related Structures:  
    5ET4, 6ENP, 5OAB, 5OGH

  • PubMed Abstract: 
  • Human RNase6 is a small cationic antimicrobial protein that belongs to the vertebrate RNaseA superfamily. All members share a common catalytic mechanism, which involves a conserved catalytic triad, constituted by two histidines and a lysine (His15/His122/Lys38 in RNase6 corresponding to His12/His119/Lys41 in RNaseA) ...

    Human RNase6 is a small cationic antimicrobial protein that belongs to the vertebrate RNaseA superfamily. All members share a common catalytic mechanism, which involves a conserved catalytic triad, constituted by two histidines and a lysine (His15/His122/Lys38 in RNase6 corresponding to His12/His119/Lys41 in RNaseA). Recently, our first crystal structure of human RNase6 identified an additional His pair (His36/His39) and suggested the presence of a secondary active site.


    Related Citations: 
    • The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement.
      Prats-Ejarque, G., Arranz-Trullen, J., Blanco, J.A., Pulido, D., Nogues, M.V., Moussaoui, M., Boix, E.
      (2016) Biochem J 473: 1523

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain. Electronic address: Ester.Boix@uab.cat.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease K6A128Homo sapiensMutation(s): 0 
Gene Names: RNASE6RNS6
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q93091 (Homo sapiens)
Explore Q93091 
Go to UniProtKB:  Q93091
PHAROS:  Q93091
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
N [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A], L [auth A], M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.405α = 90
b = 95.405β = 90
c = 95.405γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MINECOSpainSAF2015-66007-P
Generalitat de CatalunyaSpain2014 SGR 728

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references