Crystal structure of wild-type KRAS4b(1-169) in complex with GMPPNP and Mg ion

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

Ingolfsson, H.I.Neale, C.Carpenter, T.S.Shrestha, R.Lopez, C.A.Tran, T.H.Oppelstrup, T.Bhatia, H.Stanton, L.G.Zhang, X.Sundram, S.Di Natale, F.Agarwal, A.Dharuman, G.Kokkila Schumacher, S.I.L.Turbyville, T.Gulten, G.Van, Q.N.Goswami, D.Jean-Francois, F.Agamasu, C.Hettige, J.J.Travers, T.Sarkar, S.Surh, M.P.Yang, Y.Moody, A.Liu, S.Van Essen, B.C.Voter, A.F.Ramanathan, A.Hengartner, N.W.Simanshu, D.K.Stephen, A.G.Bremer, P.T.Gnanakaran, S.Glosli, J.N.Lightstone, F.C.McCormick, F.Nissley, D.V.Streitz, F.H.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2113297119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

  • Organizational Affiliation

    Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B, C
170Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.21α = 90
b = 82.33β = 112.92
c = 88.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description