6OD0

Structure of human CIB1 in complex with peptide inhibitor UNC10245092


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery and Characterization of Peptide Inhibitors for Calcium and Integrin Binding Protein 1.

Puhl, A.C.Bogart, J.W.Haberman, V.A.Larson, J.E.Godoy, A.S.Norris-Drouin, J.L.Cholensky, S.H.Leisner, T.M.Frye, S.V.Parise, L.V.Bowers, A.A.Pearce, K.H.

(2020) ACS Chem Biol 15: 1505-1516

  • DOI: https://doi.org/10.1021/acschembio.0c00144
  • Primary Citation of Related Structures:  
    6OCX, 6OD0

  • PubMed Abstract: 

    Calcium and integrin binding protein 1 (CIB1) is an EF-hand-containing, small intracellular protein that has recently been implicated in cancer cell survival and proliferation. In particular, CIB1 depletion significantly impairs tumor growth in triple-negative breast cancer (TNBC). Thus, CIB1 is a potentially attractive target for cancer chemotherapy that has yet to be validated by a chemical probe. To produce a probe molecule to the CIB1 helix 10 (H10) pocket and demonstrate that it is a viable target for molecular intervention, we employed random peptide phage display to screen and select CIB1-binding peptides. The top peptide sequence selected, UNC10245092, was produced synthetically, and binding to CIB1 was confirmed by isothermal titration calorimetry (ITC) and a time-resolved fluorescence resonance energy transfer (TR-FRET) assay. Both assays showed that the peptide bound to CIB1 with low nanomolar affinity. CIB1 was cocrystallized with UNC10245092, and the 2.1 Å resolution structure revealed that the peptide binds as an α-helix in the H10 pocket, displacing the CIB1 C-terminal H10 helix and causing conformational changes in H7 and H8. UNC10245092 was further derivatized with a C-terminal Tat-derived cell penetrating peptide (CPP) to demonstrate its effects on TNBC cells in culture, which are consistent with results of CIB1 depletion. These studies provide a first-in-class chemical tool for CIB1 inhibition in cell culture and validate the CIB1 H10 pocket for future probe and drug discovery efforts.


  • Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium and integrin-binding protein 1
A, B
191Homo sapiensMutation(s): 0 
Gene Names: CIB1CIBKIPPRKDCIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q99828 (Homo sapiens)
Explore Q99828 
Go to UniProtKB:  Q99828
PHAROS:  Q99828
GTEx:  ENSG00000185043 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99828
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide inhibitor UNC10245092C [auth D],
D [auth E]
12Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.858α = 90
b = 85.966β = 91.91
c = 67.287γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description