7NYN

Mutant Y526A of SH3 domain of JNK-interacting Protein 1 (JIP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.138 

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)63Homo sapiensMutation(s): 1 
Gene Names: MAPK8IP1IB1JIP1PRKM8IP
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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
BA [auth FFF]
EA [auth GGG]
KA [auth HHH]
N [auth AAA]
O [auth AAA]
BA [auth FFF],
EA [auth GGG],
KA [auth HHH],
N [auth AAA],
O [auth AAA],
R [auth BBB],
T [auth CCC],
Y [auth DDD]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
FA [auth GGG],
NA [auth JJJ],
Q [auth BBB],
X [auth DDD],
Z [auth DDD]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DA [auth GGG],
MA [auth III]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth EEE]
JA [auth HHH]
LA [auth III]
OA [auth KKK]
S [auth CCC]
AA [auth EEE],
JA [auth HHH],
LA [auth III],
OA [auth KKK],
S [auth CCC],
W [auth DDD]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
HA [auth HHH],
IA [auth HHH],
M [auth AAA]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth FFF]
GA [auth GGG]
P [auth AAA]
PA [auth LLL]
QA [auth LLL]
CA [auth FFF],
GA [auth GGG],
P [auth AAA],
PA [auth LLL],
QA [auth LLL],
U [auth CCC],
V [auth CCC]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.138 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.639α = 90
b = 62.485β = 90
c = 87.056γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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