3LW1

Binary complex of 14-3-3 sigma and p53 pT387-peptide

• PDB DOI: https://doi.org/10.2210/pdb3LW1/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-23 Released: 2010-03-23 
• Deposition Author(s): Schumacher, B., Mondry, J., Thiel, P., Weyand, M., Ottmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.151 
• R-Value Work: 0.126 
• R-Value Observed: 0.128 

Starting Model: experimental

Literature

Structure of the p53 C-terminus bound to 14-3-3: Implications for stabilization of the p53 tetramer

Schumacher, B., Mondry, J., Thiel, P., Weyand, M., Ottmann, C.

(2010) FEBS Lett 584: 1443-1448

• PubMed: 20206173 
• DOI: https://doi.org/10.1016/j.febslet.2010.02.065
• Primary Citation of Related Structures:  
  3LW1


• PubMed Abstract: 
  

  The adaptor protein 14-3-3 binds to and stabilizes the tumor suppressor p53 and enhances its anti-tumour activity. In the regulatory C-terminal domain of p53 several 14-3-3 binding motifs have been identified. Here, we report the crystal structure of the extreme C-terminus (residues 385-393, p53pT387) of p53 in complex with 14-3-3sigma at a resolution of 1.28A. p53pT387 is accommodated by 14-3-3 in a yet unrecognized fashion implying a rationale for 14-3-3 binding to the active p53 tetramer. The structure exhibits a potential binding site for small molecules that could stabilize the p53/14-3-3 protein complex suggesting the possibility for therapeutic intervention.

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Organizational Affiliation: 

Chemical Genomics Centre of the Max-Planck-Society, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 29.5 kDa 
• Atom Count: 2,559 
• Modelled Residue Count: 242 
• Deposited Residue Count: 262 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	253	Homo sapiens	Mutation(s): 0  Gene Names: HME1, SFN
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide of Cellular tumor antigen p53	B [auth P]	9	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637 GTEx:  ENSG00000141510

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
TPO	B [auth P]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.151 
• R-Value Work: 0.126 
• R-Value Observed: 0.128 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.32	α = 90
b = 112.32	β = 90
c = 62.66	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Schumacher, B., Mondry, J., Thiel, P., Weyand, M., Ottmann, C.

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary