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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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 dom ...

    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.,College of Life Sciences, Nankai University, Tianjin, China.,Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami, Okinawa, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCR4-NOT transcription complex subunit 6-like
A
398Homo sapiensMutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C5P
Query on C5P

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C5PIC50: 1250000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.051α = 90.00
b = 77.051β = 90.00
c = 167.650γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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