5E95

Crystal Structure of Mb(NS1)/H-Ras Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Inhibition of RAS function through targeting an allosteric regulatory site.

Spencer-Smith, R.Koide, A.Zhou, Y.Eguchi, R.R.Sha, F.Gajwani, P.Santana, D.Gupta, A.Jacobs, M.Herrero-Garcia, E.Cobbert, J.Lavoie, H.Smith, M.Rajakulendran, T.Dowdell, E.Okur, M.N.Dementieva, I.Sicheri, F.Therrien, M.Hancock, J.F.Ikura, M.Koide, S.O'Bryan, J.P.

(2017) Nat Chem Biol 13: 62-68

  • DOI: https://doi.org/10.1038/nchembio.2231
  • Primary Citation of Related Structures:  
    5E95

  • PubMed Abstract: 

    RAS GTPases are important mediators of oncogenesis in humans. However, pharmacological inhibition of RAS has proved challenging. Here we describe a functionally critical region, located outside the effector lobe of RAS, that can be targeted for inhibition. We developed NS1, a synthetic binding protein (monobody) that bound with high affinity to both GTP- and GDP-bound states of H-RAS and K-RAS but not N-RAS. NS1 potently inhibited growth factor signaling and oncogenic H-RAS- and K-RAS-mediated signaling and transformation but did not block oncogenic N-RAS, BRAF or MEK1. NS1 bound the α4-β6-α5 region of RAS, which disrupted RAS dimerization and nanoclustering and led to blocking of CRAF-BRAF heterodimerization and activation. These results establish the importance of the α4-β6-α5 interface in RAS-mediated signaling and define a previously unrecognized site in RAS for inhibiting RAS function.


  • Organizational Affiliation

    Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mb(NS1)A [auth B]97Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HRasB [auth A]168Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.897α = 86.3
b = 36.276β = 74.23
c = 54.348γ = 85.2
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM090324
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
The Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community TrustUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-23
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description