Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 22.69 kDa 
• Atom Count: 1845 
• Modelled Residue Count: 187 
• Deposited Residue Count: 193 
• Unique protein chains: 1

4H7W

Crystal Structure of Human C16orf57

• PDB DOI: 10.2210/pdb4H7W/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-21 Released: 2013-02-06 
• Deposition Author(s): Hilcenko, C., Simpson, P.J., Warren, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.154 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Literature

Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia.

Hilcenko, C., Simpson, P.J., Finch, A.J., Bowler, F.R., Churcher, M.J., Jin, L., Packman, L.C., Shlien, A., Campbell, P., Kirwan, M., Dokal, I., Warren, A.J.

(2013) Blood 121: 1028-1038

• PubMed: 23190533 
• DOI: 10.1182/blood-2012-10-461491
• Primary Citation of Related Structures:  
  4H7W


• PubMed Abstract: 
  

The recessive disorder poikiloderma with neutropenia (PN) is caused by mutations in the C16orf57 gene that encodes the highly conserved USB1 protein. Here, we present the 1.1 Å resolution crystal structure of human USB1, defining it as a member of the LigT-like superfamily of 2H phosphoesterases. We show that human USB1 is a distributive 3'-5' exoribonuclease that posttranscriptionally removes uridine and adenosine nucleosides from the 3' end of spliceosomal U6 small nuclear RNA (snRNA), directly catalyzing terminal 2', 3' cyclic phosphate formation. USB1 measures the appropriate length of the U6 oligo(U) tail by reading the position of a key adenine nucleotide (A102) and pausing 5 uridine residues downstream.We show that the 3' ends of U6 snRNA in PN patient lymphoblasts are elongated and unexpectedly carry nontemplated 3' oligo(A) tails that are characteristic of nuclear RNA surveillance targets. Thus, our study reveals a novel quality control pathway in which posttranscriptional 3'-end processing by USB1 protects U6 snRNA from targeting and destruction by the nuclear exosome. Our data implicate aberrant oligoadenylation of U6 snRNA in the pathogenesis of the leukemia predisposition disorder PN.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0406 protein C16orf57	A	193	Homo sapiens	Mutation(s): 0  Gene Names: C16orf57, USB1 EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ65 (Homo sapiens) Explore Q9BQ65  Go to UniProtKB:  Q9BQ65
PHAROS:  Q9BQ65

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.154 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.247	α = 90
b = 51.07	β = 107.44
c = 48.013	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-21 
• Released Date: 2013-02-06 
Deposition Author(s): Hilcenko, C., Simpson, P.J., Warren, A.J.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references