Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 45406.31 
• Atom Count: 2711 
• Residue Count: 398 
• Unique protein chains: 1

3NGQ

Crystal structure of the human CNOT6L nuclease domain

• DOI: 10.2210/pdb3NGQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2010-06-13 Released: 2010-07-28 
• Deposition Author(s): Wang, H., Morita, M., Yang, W., Bartlam, M., Yamamoto, T., Rao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 

Literature

Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity.

Wang, H., Morita, M., Yang, X., Suzuki, T., Yang, W., Wang, J., Ito, K., Wang, Q., Zhao, C., Bartlam, M., Yamamoto, T., Rao, Z.

(2010) Embo J. --: --

• PubMed: 20628353 
• DOI: 10.1038/emboj.2010.152
• Primary Citation of Related Structures:  
  3NGO, 3NGN


• PubMed Abstract: 
  

CCR4, an evolutionarily conserved member of the CCR4-NOT complex, is the main cytoplasmic deadenylase. It contains a C-terminal nuclease domain with homology to the endonuclease-exonuclease-phosphatase (EEP) family of enzymes. We have determined the high-resolution three-dimensional structure of the nuclease domain of CNOT6L, a human homologue of CCR4, by X-ray crystallography using the single-wavelength anomalous dispersion method. This first structure of a deadenylase belonging to the EEP family adopts a complete alpha/beta sandwich fold typical of hydrolases with highly conserved active site residues similar to APE1. The active site of CNOT6L should recognize the RNA substrate through its negatively charged surface. In vitro deadenylase assays confirm the critical active site residues and show that the nuclease domain of CNOT6L exhibits full Mg(2+)-dependent deadenylase activity with strict poly(A) RNA substrate specificity. To understand the structural basis for poly(A) RNA substrate binding, crystal structures of the CNOT6L nuclease domain have also been determined in complex with AMP and poly(A) DNA. The resulting structures suggest a molecular deadenylase mechanism involving a pentacovalent phosphate transition.

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Organizational Affiliation: 

Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, PR China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CCR4-NOT transcription complex subunit 6-like	A	398	Homo sapiens	Mutation(s): 1  Gene Names: CNOT6L (CCR4B) EC: 3.1.13.4
Find proteins for Q96LI5 (Homo sapiens) Go to Gene View: CNOT6L Go to UniProtKB:  Q96LI5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1PS	A	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE 1-(3-SULFOPROPYL) PYRIDINIUM, PPS C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.254 
• R-Value Work: 0.220 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 77.152	α = 90.00
b = 77.152	β = 90.00
c = 165.897	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SOLVE	phasing
HKL-2000	data reduction
HKL-2000	data scaling
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-13 
• Released Date: 2010-07-28 
• Deposition Author(s): Wang, H., Morita, M., Yang, W., Bartlam, M., Yamamoto, T., Rao, Z.

Revision History 

• Version 1.0: 2010-07-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance