6TWY

MAGI1_2 complexed with a phosphomimetic RSK1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study.

Gogl, G.Jane, P.Caillet-Saguy, C.Kostmann, C.Bich, G.Cousido-Siah, A.Nyitray, L.Vincentelli, R.Wolff, N.Nomine, Y.Sluchanko, N.N.Trave, G.

(2020) Structure 28: 747-759.e3

  • DOI: 10.1016/j.str.2020.03.010
  • Primary Citation of Related Structures:  
    6TWQ, 6TWU, 6TWX, 6TWY, 6TWZ

  • PubMed Abstract: 
  • Protein-protein interaction motifs are often alterable by post-translational modifications. For example, 19% of predicted human PDZ domain-binding motifs (PBMs) have been experimentally proven to be phosphorylated, and up to 82% are theoretically phosphorylatable ...

    Protein-protein interaction motifs are often alterable by post-translational modifications. For example, 19% of predicted human PDZ domain-binding motifs (PBMs) have been experimentally proven to be phosphorylated, and up to 82% are theoretically phosphorylatable. Phosphorylation of PBMs may drastically rewire their interactomes, by altering their affinities for PDZ domains and 14-3-3 proteins. The effect of phosphorylation is often analyzed by performing "phosphomimetic" mutations. Here, we focused on the PBMs of HPV16-E6 viral oncoprotein and human RSK1 kinase. We measured the binding affinities of native, phosphorylated, and phosphomimetic variants of both PBMs toward the 266 human PDZ domains. We co-crystallized all the motif variants with a selected PDZ domain to characterize the structural consequence of the different modifications. Finally, we elucidated the structural basis of PBM capture by 14-3-3 proteins. This study provides novel atomic and interactomic insights into phosphorylatable dual specificity motifs and the differential effects of phosphorylation and phosphomimetic approaches.


    Organizational Affiliation

    Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France. Electronic address: traveg@igbmc.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2A, B427Homo sapiensMutation(s): 0 
Gene Names: MAGI1AIP3BAIAP1BAP1TNRC19ANXA2ANX2ANX2L4CAL1HLPC2D
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QZ7 (Homo sapiens)
Explore Q96QZ7 
Go to UniProtKB:  Q96QZ7
PHAROS:  Q96QZ7
Find proteins for P07355 (Homo sapiens)
Explore P07355 
Go to UniProtKB:  P07355
PHAROS:  P07355
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphomimetic RSK1 peptideC11Homo sapiensMutation(s): 0 
Gene Names: RPS6KA1MAPKAPK1ARSK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15418 (Homo sapiens)
Explore Q15418 
Go to UniProtKB:  Q15418
PHAROS:  Q15418
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A], L [auth B], N [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], F [auth A], M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , O [auth B] , P [auth B] , Q [auth B] , 
G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.45α = 90
b = 96.38β = 90
c = 198.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-07-15
    Changes: Database references