9QU1 | pdb_00009qu1

Crystal structure of the human RalGAPA2 N-terminal domain with human kappaB-Ras1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The GTPase kappa B-Ras is an essential subunit of the RalGAP tumor suppressor complex.

Rasche, R.Apken, L.H.Titze, S.Michalke, E.Singh, R.K.Oeckinghaus, A.Kummel, D.

(2025) J Biological Chem 301: 110460-110460

  • DOI: https://doi.org/10.1016/j.jbc.2025.110460
  • Primary Citation Related Structures: 
    9QU1

  • PubMed Abstract: 

    κB-Ras1 and κB-Ras2 are small GTPases with non-canonical features that act as tumor suppressors downstream of Ras. Via interaction with the RalGAP (GTPase activating protein) complex, they limit activity of Ral GTPases and restrict anchorage-independent proliferation. We here present the crystal structure of κB-Ras1 in complex with the N-terminal domain of RGα2. The structure suggests a mechanism of intrinsic GTP hydrolysis of κB-Ras1 that relies on a scaffolding function of the GTPase rather than on catalytic residues, which we confirm by mutational analysis. The interaction with RGα2 is nucleotide-independent and does not involve κB-Ras1 switch regions, which establishes κB-Ras proteins as a constitutive third subunit of RalGAP complexes. Functional studies demonstrate that κB-Ras proteins are not required for RalGAP catalytic activity in vitro, but for functionality in vivo. We propose that κB-Ras may thus act as regulator of RalGAP localization and thereby control the Ras/Ral signaling pathway.


  • Organizational Affiliation
    • Institute of Biochemistry, University of Münster, Germany.

Macromolecule Content 

  • Total Structure Weight: 100.57 kDa 
  • Atom Count: 6,502 
  • Modeled Residue Count: 784 
  • Deposited Residue Count: 866 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ral GTPase-activating protein subunit alpha-2
A, B
254Homo sapiensMutation(s): 0 
Gene Names: RALGAPA2C20orf74KIAA1272
UniProt & NIH Common Fund Data Resources
Find proteins for Q2PPJ7 (Homo sapiens)
Explore Q2PPJ7 
Go to UniProtKB:  Q2PPJ7
PHAROS:  Q2PPJ7
GTEx:  ENSG00000188559 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2PPJ7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NF-kappa-B inhibitor-interacting Ras-like protein 1C,
D [auth F]
179Homo sapiensMutation(s): 0 
Gene Names: NKIRAS1KBRAS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYS0 (Homo sapiens)
Explore Q9NYS0 
Go to UniProtKB:  Q9NYS0
PHAROS:  Q9NYS0
GTEx:  ENSG00000197885 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYS0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.564α = 90
b = 63.43β = 91.263
c = 104.163γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
Aimlessdata scaling
STARANISOdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKU2531/6

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references