Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Phenothiazines inhibit S100A4 function by inducing protein oligomerization.

Malashkevich, V.N.Dulyaninova, N.G.Ramagopal, U.A.Liriano, M.A.Varney, K.M.Knight, D.Brenowitz, M.Weber, D.J.Almo, S.C.Bresnick, A.R.

(2010) Proc Natl Acad Sci U S A 107: 8605-8610

  • DOI: https://doi.org/10.1073/pnas.0913660107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    S100A4, a member of the S100 family of Ca(2+)-binding proteins, regulates carcinoma cell motility via interactions with myosin-IIA. Numerous studies indicate that S100A4 is not simply a marker for metastatic disease, but rather has a direct role in metastatic progression. These observations suggest that S100A4 is an excellent target for therapeutic intervention. Using a unique biosensor-based assay, trifluoperazine (TFP) was identified as an inhibitor that disrupts the S100A4/myosin-IIA interaction. To examine the interaction of S100A4 with TFP, we determined the 2.3 A crystal structure of human Ca(2+)-S100A4 bound to TFP. Two TFP molecules bind within the hydrophobic target binding pocket of Ca(2+)-S100A4 with no significant conformational changes observed in the protein upon complex formation. NMR chemical shift perturbations are consistent with the crystal structure and demonstrate that TFP binds to the target binding cleft of S100A4 in solution. Remarkably, TFP binding results in the assembly of five Ca(2+)-S100A4/TFP dimers into a tightly packed pentameric ring. Within each pentamer most of the contacts between S100A4 dimers occurs through the TFP moieties. The Ca(2+)-S100A4/prochlorperazine (PCP) complex exhibits a similar pentameric assembly. Equilibrium sedimentation and cross-linking studies demonstrate the cooperative formation of a similarly sized S100A4/TFP oligomer in solution. Assays examining the ability of TFP to block S100A4-mediated disassembly of myosin-IIA filaments demonstrate that significant inhibition of S100A4 function occurs only at TFP concentrations that promote S100A4 oligomerization. Together these studies support a unique mode of inhibition in which phenothiazines disrupt the S100A4/myosin-IIA interaction by sequestering S100A4 via small molecule-induced oligomerization.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A4
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
101Homo sapiensMutation(s): 0 
Gene Names: CAPLMTS1S100A4
UniProt & NIH Common Fund Data Resources
Find proteins for P26447 (Homo sapiens)
Explore P26447 
Go to UniProtKB:  P26447
PHAROS:  P26447
GTEx:  ENSG00000196154 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26447
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TFP

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth I]
AC [auth O]
BA [auth B]
BC [auth O]
AA [auth B],
AB [auth I],
AC [auth O],
BA [auth B],
BC [auth O],
CA [auth C],
CC [auth P],
DB [auth I],
EB [auth J],
FA [auth C],
FC [auth P],
GC [auth Q],
HB [auth J],
IA [auth D],
JA [auth D],
JC [auth Q],
KA [auth E],
KB [auth K],
LB [auth K],
MC [auth R],
NA [auth E],
NC [auth R],
OB [auth L],
OC [auth S],
PB [auth L],
QA [auth F],
RA [auth F],
RC [auth S],
SA [auth G],
SB [auth M],
SC [auth T],
TB [auth M],
U [auth A],
UB [auth N],
VA [auth G],
VC [auth T],
X [auth A],
XB [auth N],
YA [auth H],
ZA [auth H]
C21 H24 F3 N3 S
Query on CA

Download Ideal Coordinates CCD File 
BB [auth I]
CB [auth I]
DA [auth C]
DC [auth P]
EA [auth C]
BB [auth I],
CB [auth I],
DA [auth C],
DC [auth P],
EA [auth C],
EC [auth P],
FB [auth J],
GA [auth D],
GB [auth J],
HA [auth D],
HC [auth Q],
IB [auth K],
IC [auth Q],
JB [auth K],
KC [auth R],
LA [auth E],
LC [auth R],
MA [auth E],
MB [auth L],
NB [auth L],
OA [auth F],
PA [auth F],
PC [auth S],
QB [auth M],
QC [auth S],
RB [auth M],
TA [auth G],
TC [auth T],
UA [auth G],
UC [auth T],
V [auth A],
VB [auth N],
W [auth A],
WA [auth H],
WB [auth N],
XA [auth H],
Y [auth B],
YB [auth O],
Z [auth B],
ZB [auth O]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.794α = 90
b = 102.492β = 92.59
c = 116.629γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations