3DAC | pdb_00003dac

Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain

• PDB DOI: https://doi.org/10.2210/pdb3DAC/pdb

• Classification: CELL CYCLE
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-29 Released: 2008-09-02 
• Deposition Author(s): Popowicz, G.M., Czarna, A., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain.

Popowicz, G.M., Czarna, A., Holak, T.A.

(2008) Cell Cycle 7: 2441-2443

• PubMed: 18677113 
• DOI: https://doi.org/10.4161/cc.6365
• Primary Citation Related Structures: 
  3DAB, 3DAC


• PubMed Abstract: 
  

  The Mdmx oncoprotein has only recently emerged as a critical-independent to Mdm2-regulator of p53 activation. We have determined the crystal structure of the N-terminal domain of human Mdmx bound to a 15-residue transactivation domain peptide of human p53. The structure shows why antagonists of the Mdm2 binding to p53 are ineffective in the Mdmx-p53 interaction.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.35 kDa 
• Atom Count: 1,750 
• Modeled Residue Count: 195 
• Deposited Residue Count: 302 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mdm4 protein	A [auth M], C [auth A]	130	Danio rerio	Mutation(s): 2  Gene Names: mdm4, mdmx
UniProt
Find proteins for Q7ZUW7 (Danio rerio) Explore Q7ZUW7  Go to UniProtKB:  Q7ZUW7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	B [auth P], D [auth B]	21	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.43	α = 90
b = 30.81	β = 107.43
c = 70.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Popowicz, G.M., Czarna, A., Holak, T.A.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-11-06
  Changes: Data collection, Database references
• Version 1.4: 2021-11-10
  Changes: Database references
• Version 1.5: 2023-11-01
  Changes: Data collection, Refinement description