Crystal structure of the human CNOT6L nuclease domain in complex with AMP

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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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 

  • DOI: https://doi.org/10.1038/emboj.2010.152
  • Primary Citation of Related Structures:  
    3NGN, 3NGO, 3NGQ

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 6-like398Homo sapiensMutation(s): 0 
Gene Names: CNOT6LCCR4B
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LI5 (Homo sapiens)
Explore Q96LI5 
Go to UniProtKB:  Q96LI5
GTEx:  ENSG00000138767 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LI5
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.955α = 90
b = 76.955β = 90
c = 165.654γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations