5ET4

Structure of RNase A-K7H/R10H in complex with 3'-CMP

• PDB DOI: https://doi.org/10.2210/pdb5ET4/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2015-11-17 Released: 2016-11-30 
• Deposition Author(s): Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.321 
• R-Value Work: 0.224 
• R-Value Observed: 0.229 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.2 kDa 
• Atom Count: 4,343 
• Modelled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B, C, D	124	Bos taurus	Mutation(s): 2  Gene Names: RNASE1, RNS1 EC: 3.1.27.5
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C3P	E [auth A], F [auth B], G [auth C], I [auth D]	CYTIDINE-3'-MONOPHOSPHATE C9 H14 N3 O8 P UOOOPKANIPLQPU-XVFCMESISA-N
MPD	H [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C3P	BindingDB:  5ET4	Ki: min: 2.01e+4, max: 1.03e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.321 
• R-Value Work: 0.224 
• R-Value Observed: 0.229 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.366	α = 90
b = 32.281	β = 125.71
c = 106.963	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Blanco, J.A., Salazar, V.A., Moussaoui, M., Boix, E.

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Funding Organization	Location	Grant Number
	Spain	--

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Source and taxonomy
• Version 1.2: 2019-07-17
  Changes: Data collection
• Version 1.3: 2021-02-24
  Changes: Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description