Crystal structure of human CNOT6L in complex with neomycin

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Structural basis for inhibition of the deadenylase activity of human CNOT6L

Zhang, Q.Yan, D.Guo, E.Ding, B.Yang, W.Liu, R.Yamamoto, T.Bartlam, M.

(2016) FEBS Lett 590: 1270-1279

  • DOI: https://doi.org/10.1002/1873-3468.12160
  • Primary Citation of Related Structures:  
    5DV2, 5DV4

  • PubMed Abstract: 

    Human CNOT6L/CCR4, a member of the endonuclease-exonuclease-phosphatase (EEP) family enzymes, is one of the two deadenylase enzymes in the conserved CCR4-NOT complex. Here, we report inhibitor-bound crystal structures of the human CNOT6L nuclease domain in complex with the nucleotide CMP and the aminoglycoside neomycin. Deadenylase activity assays show that nucleotides are effective inhibitors of both CNOT6L and CNOT7, with AMP more effective than other nucleotides, and that neomycin is a weak deadenylase inhibitor. Structural analysis shows that all inhibitors occupy the substrate and magnesium-binding sites of CNOT6L, suggesting that inhibitors compete with both substrate and divalent magnesium ions for overlapping binding sites.

  • Organizational Affiliation

    College of Life Sciences, Nankai University, Tianjin, 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
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
Binding Affinity Annotations 
IDSourceBinding Affinity
NMY Binding MOAD:  5DV4 IC50: 3.37e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.388α = 90
b = 77.388β = 90
c = 167.188γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science & Technology 973 ProjectChina2014CB560709

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references