6JRP

Crystal structure of CIC-HMG-ETV5-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.301 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The crystal structure of Capicua HMG-box domain complexed with the ETV5-DNA and its implications for Capicua-mediated cancers.

Lee, H.Song, J.J.

(2019) FEBS J 286: 4951-4963

  • DOI: 10.1111/febs.15008
  • Primary Citation of Related Structures:  
    6JRP

  • PubMed Abstract: 
  • Capicua (CIC) is a transcriptional repressor and functions downstream of the receptor tyrosine kinase (RTK) signaling pathway. Somatic mutations found in the HMG-box DNA binding domain in CIC have been implicated in several cancers such as oligodendroglioma, oligoastrocytoma, and adenocarcinoma ...

    Capicua (CIC) is a transcriptional repressor and functions downstream of the receptor tyrosine kinase (RTK) signaling pathway. Somatic mutations found in the HMG-box DNA binding domain in CIC have been implicated in several cancers such as oligodendroglioma, oligoastrocytoma, and adenocarcinoma. However, the molecular basis of the DNA binding of CIC and the effect of the somatic mutations found in cancers on DNA binding have not been investigated. Here, we report the crystal structure of the HMG-box domain of CIC complexed with its target DNA, the promoter of Ets Translocation Variant 5 (ETV5). The structure shows that the HMG-box domain has an L-shaped structure and recognizes the minor groove leading to DNA bending. Our structure combined with an electrophoretic mobility shift assay (EMSA) revealed that cancer-associated mutations in the HMG-box domain abrogate the interaction with DNA. These results provide the molecular insight into the DNA binding of CIC and reveal the effects of carcinogenic mutations on DNA binding.


    Organizational Affiliation

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein capicua homologA, D, G, J80Homo sapiensMutation(s): 0 
Gene Names: CICKIAA0306
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RK0 (Homo sapiens)
Explore Q96RK0 
Go to UniProtKB:  Q96RK0
PHAROS:  Q96RK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RK0
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3')B, E, H, K11Homo sapiens
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')C, F, I, L11Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, D, G, J L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.301 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.082α = 90
b = 66.082β = 90
c = 158.285γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2016K1A1A2912057
National Research Foundation (Korea)Korea, Republic Of2016R1A2B3006293

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Database references