Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 28.45 kDa 
• Atom Count: 1856 
• Residue Count: 196 
• Unique protein chains: 1

3T0O

Crystal Structure Analysis of Human RNase T2

• DOI: 10.2210/pdb3T0O/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2011-07-20 Released: 2012-07-11 
• Deposition Author(s): Thorn, A., Kraetzner, R., Steinfeld, R., Sheldrick, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.190 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Structure and activity of the only human RNase T2.

Thorn, A., Steinfeld, R., Ziegenbein, M., Grapp, M., Hsiao, H.H., Urlaub, H., Sheldrick, G.M., Gartner, J., Kratzner, R.

(2012) Nucleic Acids Res 40: 8733-8742

• PubMed: 22735700 
• DOI: 10.1093/nar/gks614
• Primary Citation of Related Structures:  
  3T0O


• PubMed Abstract: 
  

Mutations in the gene of human RNase T2 are associated with white matter disease of the human brain. Although brain abnormalities (bilateral temporal lobe cysts and multifocal white matter lesions) and clinical symptoms (psychomotor impairments, spasticity and epilepsy) are well characterized, the pathomechanism of RNase T2 deficiency remains unclear. RNase T2 is the only member of the Rh/T2/S family of acidic hydrolases in humans. In recent years, new functions such as tumor suppressing properties of RNase T2 have been reported that are independent of its catalytic activity. We determined the X-ray structure of human RNase T2 at 1.6 Å resolution. The α+β core fold shows high similarity to those of known T2 RNase structures from plants, while, in contrast, the external loop regions show distinct structural differences. The catalytic features of RNase T2 in presence of bivalent cations were analyzed and the structural consequences of known clinical mutations were investigated. Our data provide further insight into the function of human RNase T2 and may prove useful in understanding its mode of action independent of its enzymatic activity.

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Organizational Affiliation: 

Department of Structural Chemistry, University of Göttingen, 37075 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease T2	A	238	Homo sapiens	Mutation(s): 0  Gene Names: RNASET2, RNASE6PL EC: 3.1.27.1 (PDB Primary Data), 4.6.1.19 (UniProt)
Find proteins for O00584 (Homo sapiens) Explore O00584  Go to UniProtKB:  O00584
NIH Common Fund Data Resources
PHAROS:  O00584 GTEx:  ENSG00000026297

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.190 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.2	α = 90
b = 67.4	β = 90.81
c = 47.9	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-20 
• Released Date: 2012-07-11 
Deposition Author(s): Thorn, A., Kraetzner, R., Steinfeld, R., Sheldrick, G.

Revision History 

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Database references
• Version 1.2: 2012-10-10
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary