7TVF | pdb_00007tvf

Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome.

Bonsor, D.A.Alexander, P.Snead, K.Hartig, N.Drew, M.Messing, S.Finci, L.I.Nissley, D.V.McCormick, F.Esposito, D.Rodriguez-Viciana, P.Stephen, A.G.Simanshu, D.K.

(2022) Nat Struct Mol Biol 29: 966-977

  • DOI: https://doi.org/10.1038/s41594-022-00841-4
  • Primary Citation Related Structures: 
    7TVF, 7TVG

  • PubMed Abstract: 

    SHOC2 acts as a strong synthetic lethal interactor with MEK inhibitors in multiple KRAS cancer cell lines. SHOC2 forms a heterotrimeric complex with MRAS and PP1C that is essential for regulating RAF and MAPK-pathway activation by dephosphorylating a specific phosphoserine on RAF kinases. Here we present the high-resolution crystal structure of the SHOC2-MRAS-PP1C (SMP) complex and apo-SHOC2. Our structures reveal that SHOC2, MRAS, and PP1C form a stable ternary complex in which all three proteins synergistically interact with each other. Our results show that dephosphorylation of RAF substrates by PP1C is enhanced upon interacting with SHOC2 and MRAS. The SMP complex forms only when MRAS is in an active state and is dependent on SHOC2 functioning as a scaffolding protein in the complex by bringing PP1C and MRAS together. Our results provide structural insights into the role of the SMP complex in RAF activation and how mutations found in Noonan syndrome enhance complex formation, and reveal new avenues for therapeutic interventions.


  • Organizational Affiliation
    • NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 249.1 kDa 
  • Atom Count: 16,911 
  • Modeled Residue Count: 1,968 
  • Deposited Residue Count: 2,180 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunitA [auth F],
B [auth C]
329Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein M-RasC [auth E],
D [auth B]
179Homo 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: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat protein SHOC-2E [auth A],
F [auth D]
582Homo sapiensMutation(s): 0 
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

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
(Subject of Investigation/LOI)

Query on GNP



Download:Ideal Coordinates CCD File
T [auth E],
Z [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth B]
HA [auth A]
I [auth F]
J [auth F]
OA [auth D]
BA [auth B],
HA [auth A],
I [auth F],
J [auth F],
OA [auth D],
PA [auth D],
Q [auth C],
W [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4

Query on PO4



Download:Ideal Coordinates CCD File
N [auth F]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth B]
DA [auth A]
EA [auth A]
FA [auth A]
G [auth F]
AA [auth B],
DA [auth A],
EA [auth A],
FA [auth A],
G [auth F],
GA [auth A],
H [auth F],
LA [auth D],
MA [auth D],
NA [auth D],
P [auth C],
U [auth E],
V [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
K [auth F],
L [auth F],
R [auth C],
S [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
IA [auth A],
JA [auth A],
KA [auth A],
O [auth F],
QA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
CA [auth B],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth F],
Y [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.938α = 90
b = 129.938β = 90
c = 326.795γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Database references
  • Version 1.3: 2022-10-26
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description