3UZD

Crystal structure of 14-3-3 GAMMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report



Literature

Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock.

Xu, C.Jin, J.Bian, C.Lam, R.Tian, R.Weist, R.You, L.Nie, J.Bochkarev, A.Tempel, W.Tan, C.S.Wasney, G.A.Vedadi, M.Gish, G.D.Arrowsmith, C.H.Pawson, T.Yang, X.J.Min, J.

(2012) Sci Signal 5: ra39-ra39

  • DOI: 10.1126/scisignal.2002979
  • Primary Citation of Related Structures:  
    3SO8, 3V2X, 3V2O, 3V30, 3V31, 3UXG, 3UZD

  • PubMed Abstract: 
  • Ankyrin repeat family A protein 2 (ANKRA2) interacts with the plasma membrane receptor megalin and the class IIa histone deacetylases HDAC4 and HDAC5. We report that the ankyrin repeat domains of ANKRA2 and its close paralog regulatory factor X-assoc ...

    Ankyrin repeat family A protein 2 (ANKRA2) interacts with the plasma membrane receptor megalin and the class IIa histone deacetylases HDAC4 and HDAC5. We report that the ankyrin repeat domains of ANKRA2 and its close paralog regulatory factor X-associated ankyrin-containing protein (RFXANK) recognize a PxLPxI/L motif found in diverse binding proteins, including HDAC4, HDAC5, HDAC9, megalin, and regulatory factor X, 5 (RFX5). Crystal structures of the ankyrin repeat domain of ANKRA2 in complex with its binding peptides revealed that each of the middle three ankyrin repeats of ANKRA2 recognizes a residue from the PxLPxI/L motif in a tumbler-lock binding mode, with ANKRA2 acting as the lock and the linear binding motif serving as the key. Structural analysis showed that three disease-causing mutations in RFXANK affect residues that are critical for binding to RFX5. These results suggest a fundamental principle of longitudinal recognition of linear sequences by a repeat-type domain. In addition, phosphorylation of serine 350, a residue embedded within the PxLPxI/L motif of HDAC4, impaired the binding of ANKRA2 but generated a high-affinity docking site for 14-3-3 proteins, which may help sequester this HDAC in the cytoplasm. Thus, the binding preference of the PxLPxI/L motif is signal-dependent. Furthermore, proteome-wide screening suggested that a similar phosphorylation-dependent switch may operate in other pathways. Together, our findings uncover a previously uncharacterized sequence- and signal-dependent peptide recognition mode for a repeat-type protein domain.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
14-3-3 protein gammaA248Homo sapiensMutation(s): 0 
Gene Names: YWHAG
Find proteins for P61981 (Homo sapiens)
Explore P61981 
Go to UniProtKB:  P61981
NIH Common Fund Data Resources
PHAROS  P61981
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 4B17Homo sapiensMutation(s): 0 
Gene Names: HDAC4KIAA0288
EC: 3.5.1.98
Find proteins for P56524 (Homo sapiens)
Explore P56524 
Go to UniProtKB:  P56524
NIH Common Fund Data Resources
PHAROS  P56524
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.511α = 90
b = 79.23β = 90
c = 122.232γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release