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 7TYG | pdb_00007tyg

Structure of the human leucine rich repeat protein SHOC2, residues 80-582


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TYG

This is version 1.3 of the entry. See complete history. 

Literature

Structure of the MRAS-SHOC2-PP1C phosphatase complex.

Hauseman, Z.J., Fodor, M., Dhembi, A., Viscomi, J., Egli, D., Bleu, M., Katz, S., Park, E., Jang, D.M., Porter, K.A., Meili, F., Guo, H., Kerr, G., Molle, S., Velez-Vega, C., Beyer, K.S., Galli, G.G., Maira, S.M., Stams, T., Clark, K., Eck, M.J., Tordella, L., Thoma, C.R., King, D.A.

(2022) Nature 609: 416-423

  • DOI: https://doi.org/10.1038/s41586-022-05086-1
  • Primary Citation Related Structures: 
    7TXH, 7TYG

  • PubMed Abstract: 

    RAS-MAPK signalling is fundamental for cell proliferation and is altered in most human cancers 1-3 . However, our mechanistic understanding of how RAS signals through RAF is still incomplete. Although studies revealed snapshots for autoinhibited and active RAF-MEK1-14-3-3 complexes 4 , the intermediate steps that lead to RAF activation remain unclear. The MRAS-SHOC2-PP1C holophosphatase dephosphorylates RAF at serine 259, resulting in the partial displacement of 14-3-3 and RAF-RAS association 3,5,6 . MRAS, SHOC2 and PP1C are mutated in rasopathies-developmental syndromes caused by aberrant MAPK pathway activation 6-14 -and SHOC2 itself has emerged as potential target in receptor tyrosine kinase (RTK)-RAS-driven tumours 15-18 . Despite its importance, structural understanding of the SHOC2 holophosphatase is lacking. Here we determine, using X-ray crystallography, the structure of the MRAS-SHOC2-PP1C complex. SHOC2 bridges PP1C and MRAS through its concave surface and enables reciprocal interactions between all three subunits. Biophysical characterization indicates a cooperative assembly driven by the MRAS GTP-bound active state, an observation that is extendible to other RAS isoforms. Our findings support the concept of a RAS-driven and multi-molecular model for RAF activation in which individual RAS-GTP molecules recruit RAF-14-3-3 and SHOC2-PP1C to produce downstream pathway activation. Importantly, we find that rasopathy and cancer mutations reside at protein-protein interfaces within the holophosphatase, resulting in enhanced affinities and function. Collectively, our findings shed light on a fundamental mechanism of RAS biology and on mechanisms of clinically observed enhanced RAS-MAPK signalling, therefore providing the structural basis for therapeutic interventions.


  • Organizational Affiliation: 
    • Novartis Institutes for BioMedical Research, Cambridge, MA, USA. zachary.hauseman@novartis.com.

Macromolecule Content 

  • Total Structure Weight: 113.5 kDa 
  • Atom Count: 8,414 
  • Modeled Residue Count: 987 
  • Deposited Residue Count: 1,010 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat protein SHOC-2
A, B
505Homo sapiensMutation(s): 0 
Gene Names: SHOC2, KIAA0862
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ13 (Homo sapiens)
Explore Q9UQ13 
Go to UniProtKB:  Q9UQ13
PHAROS:  Q9UQ13
GTEx:  ENSG00000108061 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQ13
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.35α = 90
b = 102.88β = 101.738
c = 120.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2022-09-21
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description