7DVD

The crystal structure of p53 DNA binding domain and PUMA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis of the p53 DNA binding domain and PUMA complex.

Han, C.W.Lee, H.N.Jeong, M.S.Park, S.Y.Jang, S.B.

(2021) Biochem Biophys Res Commun 548: 39-46

  • DOI: 10.1016/j.bbrc.2021.02.049
  • Primary Citation of Related Structures:  
    7DVD

  • PubMed Abstract: 
  • PUMA (p53-upregulated modulator of apoptosis) is localized in mitochondria and a direct target in p53-mediated apoptosis. p53 elicits mitochondrial apoptosis via transcription-dependent and independent mechanisms. p53 is known to induce apoptosis via the transcriptional induction of PUMA, which encodes proapoptotic BH3-only members of the Bcl-2 protein family ...

    PUMA (p53-upregulated modulator of apoptosis) is localized in mitochondria and a direct target in p53-mediated apoptosis. p53 elicits mitochondrial apoptosis via transcription-dependent and independent mechanisms. p53 is known to induce apoptosis via the transcriptional induction of PUMA, which encodes proapoptotic BH3-only members of the Bcl-2 protein family. However, the transcription-independent mechanisms of human PUMA remain poorly defined. For example, it is not known whether PUMA interacts directly with the DNA binding domain (DBD: residues 92-293) of p53 in vitro. Here, the structure of the complex between the DBD of p53 and PUMA peptide was elucidated by X-ray crystallography. Isothermal titration calorimetry showed that PUMA peptide binds strongly with p53 DBD, and the crystal structure of p53-PUMA peptide complex revealed it contains four molecules of p53 DBD and one PUMA peptide per asymmetric unit in space group P 1 . PUMA peptide bound to the N-terminal residues of p53 DBD. A cell proliferation assay demonstrated PUMA peptide inhibited the growth of a lung cancer cell line. These results contribute to understanding of the mechanism responsible for p53-mediated apoptosis.


    Related Citations: 
    • In vitro binding properties of tumor suppressor p53 with PUMA and NOXA
      Park, S.Y., Jang, S.B.
      (2012) Biochem Biophys Res Commun 420(2): 350

    Organizational Affiliation

    Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea. Electronic address: sbjang@pusan.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53A, B, C, D205Homo sapiensMutation(s): 0 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-binding component 3, isoforms 1/2E15Homo sapiensMutation(s): 0 
Gene Names: BBC3PUMA
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXH1 (Homo sapiens)
Explore Q9BXH1 
Go to UniProtKB:  Q9BXH1
PHAROS:  Q9BXH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXH1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.273 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.612α = 89.939
b = 73.411β = 89.823
c = 84.408γ = 89.996
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXdata processing
Cootdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2018R1D1A1B07043701

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release