4CZ6 | pdb_00004cz6

Truncated tetramerization domain of zebrafish p53 (crystal form II)

• PDB DOI: https://doi.org/10.2210/pdb4CZ6/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-16 Released: 2014-08-27 
• Deposition Author(s): Joerger, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.184 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Tracing the Evolution of the P53 Tetramerization Domain

Joerger, A.C., Wilcken, R., Andreeva, A.

(2014) Structure 22: 1301

• PubMed: 25185827 
• DOI: https://doi.org/10.1016/j.str.2014.07.010
• Primary Citation Related Structures: 
  4CZ5, 4CZ6, 4CZ7, 4D1L, 4D1M


• PubMed Abstract: 
  

  The tetrameric transcription factors p53, p63, and p73 evolved from a common ancestor and play key roles in tumor suppression and development. Surprisingly, p63 and p73 require a second helix in their tetramerization domain for the formation of stable tetramers that is absent in human p53, raising questions about the evolutionary processes leading to diversification. Here we determined the crystal structure of the zebrafish p53 tetramerization domain, which contains a second helix, reminiscent of p63 and p73, combined with p53-like features. Through comprehensive phylogenetic analyses, we systematically traced the evolution of vertebrate p53 family oligomerization domains back to the beginning of multicellular life. We provide evidence that their last common ancestor also had an extended p63/p73-like domain and pinpoint evolutionary events that shaped this domain during vertebrate radiation. Domain compaction and transformation of a structured into a flexible, intrinsically disordered region may have contributed to the expansion of the human p53 interactome.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: [e-mail].
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.3 kDa 
• Atom Count: 1,084 
• Modeled Residue Count: 120 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULAR TUMOR ANTIGEN P53	A, B, C, D	33	Danio rerio	Mutation(s): 0
UniProt
Find proteins for P79734 (Danio rerio) Explore P79734  Go to UniProtKB:  P79734

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.184 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.529	α = 90
b = 57.529	β = 90
c = 96.875	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Joerger, A.C.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-22
  Changes: Data collection, Experimental preparation
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other