5OAB

A novel crystal form of human RNase6 at atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb5OAB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-21 Released: 2018-08-01 
• Deposition Author(s): Prats-Ejarque, G., Moussaoui, M., Boix, E.
• Funding Organization(s): MINECO, Generalitat de Catalunya

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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 

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

• PubMed: 30287244 
• DOI: https://doi.org/10.1016/j.bbagen.2018.09.021
• Primary Citation of Related Structures:  
  5ET4, 5OAB, 5OGH, 6ENP


• 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). Recently, our first crystal structure of human RNase6 identified an additional His pair (His36/His39) and suggested the presence of a secondary active site.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 15.59 kDa 
• Atom Count: 1,554 
• Modelled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease K6	A	128	Homo sapiens	Mutation(s): 0  Gene Names: RNASE6, RNS6 EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q93091 (Homo sapiens) Explore Q93091  Go to UniProtKB:  Q93091
PHAROS:  Q93091 GTEx:  ENSG00000169413

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	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
K	N [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 95.405	α = 90
b = 95.405	β = 90
c = 95.405	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Prats-Ejarque, G., Moussaoui, M., Boix, E.

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Funding Organization	Location	Grant Number
MINECO	Spain	SAF2015-66007-P
Generalitat de Catalunya	Spain	2014 SGR 728

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description