7TXH | pdb_00007txh

Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TXH

Ligand Structure Quality Assessment 


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: 225.67 kDa 
  • Atom Count: 17,319 
  • Modeled Residue Count: 1,920 
  • Deposited Residue Count: 1,964 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein M-Ras
A, D
180Homo sapiensMutation(s): 1 
Gene Names: MRASRRAS3
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14807 (Homo sapiens)
Explore O14807 
Go to UniProtKB:  O14807
PHAROS:  O14807
GTEx:  ENSG00000158186 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14807
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat protein SHOC-2
B, E
505Homo sapiensMutation(s): 1 
Gene Names: SHOC2KIAA0862
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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C, F
297Homo sapiensMutation(s): 0 
Gene Names: PPP1CAPPP1A
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens)
Explore P62136 
Go to UniProtKB:  P62136
PHAROS:  P62136
GTEx:  ENSG00000172531 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62136
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP

Query on GNP



Download:Ideal Coordinates CCD File
G [auth A],
S [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
BA [auth E],
EA [auth F],
O [auth C],
R [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth E]
FA [auth F]
GA [auth F]
HA [auth F]
I [auth A]
AA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
P [auth C],
Q [auth C],
U [auth D],
V [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
CA [auth F],
DA [auth F],
M [auth C],
N [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.959α = 90
b = 115.755β = 100.314
c = 137.804γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
PHASERphasing
autoPROCdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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