5DV2

Crystal structure of human CNOT6L in complex with cytidine-5'-monophosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Literature

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: 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 ...

    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: 

    State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 6-likeA398Homo sapiensMutation(s): 0 
Gene Names: CNOT6L, CCR4B
EC: 3.1.13.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LI5 (Homo sapiens)
Explore Q96LI5 
Go to UniProtKB:  Q96LI5
PHAROS:  Q96LI5
GTEx:  ENSG00000138767 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LI5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C5P
Query on C5P
Download Ideal Coordinates CCD File 
B [auth A]CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C5P Binding MOAD:  5DV2 IC50: 1.25e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.051α = 90
b = 77.051β = 90
c = 167.65γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-09-21 
  • Released Date: 2016-05-18 
    • Deposition Author(s): Zhang, Q., Bartlam, M.
Funding OrganizationLocationGrant Number
Ministry of Science & Technology 973 ProjectChina2014CB560709

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release