6T58

Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure Determination of the Transactivation Domain of p53 in Complex with S100A4 Using Annexin A2 as a Crystallization Chaperone.

Ecsedi, P., Gogl, G., Hof, H., Kiss, B., Harmat, V., Nyitray, L.

(2020) Structure 28: 943-953.e4

  • DOI: 10.1016/j.str.2020.05.001
  • Primary Citation of Related Structures:  
    6T58

  • PubMed Abstract: 

    • To fully understand the environmental factors that influence crystallization is an enormous task, therefore crystallographers are still forced to work "blindly" trying as many crystallizing conditions and mutations to improve crystal packing as possible. Numerous times these random attempts simply fail even when using state-of-the-art techniques ...

    To fully understand the environmental factors that influence crystallization is an enormous task, therefore crystallographers are still forced to work "blindly" trying as many crystallizing conditions and mutations to improve crystal packing as possible. Numerous times these random attempts simply fail even when using state-of-the-art techniques. As an alternative, crystallization chaperones, having good crystal-forming properties, can be invoked. Today, the almost exclusively used such protein is the maltose-binding protein (MBP) and crystallographers need other widely applicable options. Here, we introduce annexin A2 (ANXA2), which has just as good, if not better, crystal-forming ability than the wild-type MBP. Using ANXA2 as heterologous fusion partner, we were able to solve the atomic resolution structure of a challenging crystallization target, the transactivation domain (TAD) of p53 in complex with the metastasis-associated protein S100A4. p53 TAD forms an asymmetric fuzzy complex with the symmetric S1004 and could interfere with its function.

    Organizational Affiliation: 

    Department of Biochemistry, ELTE Eötvös Loránd University, Budapest 1117, Hungary. Electronic address: nyitray@elte.hu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53,Protein S100-A4,Protein S100-A4,Annexin A2A, B553Homo sapiensMutation(s): 1 
Gene Names: TP53, P53, S100A4, CAPL, MTS1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
Find proteins for P07355 (Homo sapiens)
Explore P07355 
Go to UniProtKB:  P07355
PHAROS:  P07355
Find proteins for P26447 (Homo sapiens)
Explore P26447 
Go to UniProtKB:  P26447
PHAROS:  P26447
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP26447P04637P07355
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
O [auth B],
P [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.96α = 90
b = 62.77β = 90.26
c = 106.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Hungarian Academy of SciencesHungary--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Database references, Derived calculations
  • Version 1.3: 2022-12-07
    Changes: Advisory, Database references, Derived calculations