9JEJ | pdb_00009jej

Crystal structure of human EP300 KIX domain (L644C mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.281 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: in silico
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Literature

Comparative crystal structure analysis of the human EP300 and CBP KIX domains.

Cho, S.E.Lee, Y.Kim, J.I.Jung, K.Y.Jeong, H.Park, H.W.Lee, B.I.

(2024) Biochem Biophys Res Commun 741: 151064-151064

  • DOI: https://doi.org/10.1016/j.bbrc.2024.151064
  • Primary Citation of Related Structures:  
    9JEJ

  • PubMed Abstract: 

    Small-cell lung cancer (SCLC) is highly lethal because the tumors grow and metastasize rapidly. Effective treatments for SCLC are lacking currently. A recent study demonstrated that the E1A binding protein P300 (EP300) KIX domain has pro-tumorigenic activity and is selectively involved in the development and growth of SCLC. These findings suggest the possibility of developing small-molecule inhibitors of EP300 KIX as new targeted therapies for SCLC. In this study, we reported the crystal structure of the human EP300 KIX domain at 2.9 Å resolution except for a flexible loop and C-terminal end. The overall structure was almost identical to that of the cAMP response element-binding protein (CBP) KIX. Nine EP300 KIX residues were different from those of CBP KIX. Among these non-strictly conserved residues, Ala627, which corresponds to Asp647 in CBP KIX, reduces the negative surface potential. Asn581 and Arg613 contributed to the formation of additional hydrogen bonds in the EP300 KIX structure. Further structural analysis revealed that the hydrophobic residues that form the allosteric network in CBP KIX were well conserved in the EP300 KIX structure. This study lays the groundwork for structure-based drug design for SCLC.


  • Organizational Affiliation
    • Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase p300
A, B, C
101Homo sapiensMutation(s): 1 
Gene Names: EP300P300
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
PHAROS:  Q09472
GTEx:  ENSG00000100393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09472
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.281 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.342α = 90
b = 96.342β = 90
c = 136.256γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of2310200

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release