6P0J

Crystal structure of GDP-bound human RalA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

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This is version 1.3 of the entry. See complete history


Literature

Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases.

Bum-Erdene, K.Liu, D.Gonzalez-Gutierrez, G.Ghozayel, M.K.Xu, D.Meroueh, S.O.

(2020) Proc Natl Acad Sci U S A 117: 7131-7139

  • DOI: https://doi.org/10.1073/pnas.1913654117
  • Primary Citation of Related Structures:  
    6P0I, 6P0J, 6P0K, 6P0L, 6P0M, 6P0N, 6P0O

  • PubMed Abstract: 

    Ral (Ras-like) GTPases are directly activated by oncogenic Ras GTPases. Mutant K-Ras (G12C) has enabled the development of covalent K-Ras inhibitors currently in clinical trials. However, Ral, and the overwhelming majority of mutant oncogenic K-Ras, are devoid of a druggable pocket and lack an accessible cysteine for the development of a covalent inhibitor. Here, we report that covalent bond formation by an aryl sulfonyl fluoride electrophile at a tyrosine residue (Tyr-82) inhibits guanine exchange factor Rgl2-mediated nucleotide exchange of Ral GTPase. A high-resolution 1.18-Å X-ray cocrystal structure shows that the compound binds to a well-defined binding site in RalA as a result of a switch II loop conformational change. The structure, along with additional high-resolution crystal structures of several analogs in complex with RalA, confirm the importance of key hydrogen bond anchors between compound sulfone oxygen atoms and Ral backbone nitrogen atoms. Our discovery of a pocket with features found on known druggable sites and covalent modification of a bystander tyrosine residue present in Ral and Ras GTPases provide a strategy that could lead to therapeutic agent targeting oncogenic Ras mutants that are devoid of a cysteine nucleophile.


  • Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Ral-AA [auth B]186Homo sapiensMutation(s): 0 
Gene Names: RALARAL
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P11233 (Homo sapiens)
Explore P11233 
Go to UniProtKB:  P11233
GTEx:  ENSG00000006451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11233
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.948α = 90
b = 104.809β = 90
c = 55.22γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
PHENIXmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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 StatesR01CA197928

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2020-04-15
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description