9QWP | pdb_00009qwp

Structure of the human RalGAP2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of the RalGAP tumor suppressor complex.

Rasche, R.Klink, B.U.Apken, L.H.Michalke, E.Chen, M.Oeckinghaus, A.Gatsogiannis, C.Kummel, D.

(2025) Nat Commun 16: 7002-7002

  • DOI: https://doi.org/10.1038/s41467-025-61743-9
  • Primary Citation of Related Structures:  
    9QWP

  • PubMed Abstract: 

    The RalGAP (GTPase activating protein) complexes are negative regulators of the Ral GTPases and thus crucial components that counteract oncogenic Ras signaling. However, no structural information on the architecture of this tumor suppressor complex is available hampering a mechanistic understanding of its functionality. Here, we present a cryo-EM structure of RalGAP that reveals an extended 58 nm tetrameric architecture comprising two heterodimers of the RalGAPα and RalGAPβ subunits. We show that the catalytic domain of RalGAPα requires stabilization by a unique domain of RalGAPβ, providing the molecular basis for why RalGAP complexes are obligatory heterodimers. Formation of RalGAP tetramers is not required for activity in vitro, but essential for function of the complex in vivo. Structural analysis of RalGAP subunit variants reported in cancer patients suggests effects on complex formation and thus functional relevance, emphasizing the significance of the obtained structural information for medical research.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ral GTPase-activating protein subunit alpha-2
A, D
1,899Homo 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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ral GTPase-activating protein subunit beta
B, C
1,528Homo sapiensMutation(s): 0 
Gene Names: RALGAPBKIAA1219
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X10 (Homo sapiens)
Explore Q86X10 
Go to UniProtKB:  Q86X10
PHAROS:  Q86X10
GTEx:  ENSG00000170471 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86X10
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5
MODEL REFINEMENTPHENIX1.21.1_5286
MODEL REFINEMENTCoot0.9.8.95
MODEL REFINEMENTISOLDE1.7

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKU2531/2
German Research Foundation (DFG)GermanyKU2531/6
German Research Foundation (DFG)Germany496113311
German Research Foundation (DFG)GermanyCRC 1348 A15
German Research Foundation (DFG)GermanyCRC1430 A04
German Research Foundation (DFG)GermanyINST 211/667-1

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references
  • Version 1.2: 2025-08-13
    Changes: Data collection, Database references