7NYO

Mutant A541L of SH3 domain of JNK-interacting Protein 1 (JIP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7NYK


Literature

Visualizing protein breathing motions associated with aromatic ring flipping.

Marino Perez, L.Ielasi, F.S.Bessa, L.M.Maurin, D.Kragelj, J.Blackledge, M.Salvi, N.Bouvignies, G.Palencia, A.Jensen, M.R.

(2022) Nature 602: 695-700

  • DOI: https://doi.org/10.1038/s41586-022-04417-6
  • Primary Citation of Related Structures:  
    7NYK, 7NYL, 7NYM, 7NYN, 7NYO, 7NZB, 7NZC, 7NZD

  • PubMed Abstract: 

    Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180° rotations-despite their role in maintaining the protein fold 1-3 . It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events 1 . However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.


  • Organizational Affiliation

    Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SH3 domain of JNK-interacting Protein 1 (JIP1)A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
63Homo sapiensMutation(s): 1 
Gene Names: MAPK8IP1IB1JIP1PRKM8IP
EC: 3.1.3.36
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQF2 (Homo sapiens)
Explore Q9UQF2 
Go to UniProtKB:  Q9UQF2
PHAROS:  Q9UQF2
GTEx:  ENSG00000121653 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQF2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.093α = 90
b = 67.104β = 126.701
c = 59.142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceRC18114CC
Agence Nationale de la Recherche (ANR)FranceMAPKAssembly

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description