# Structure and mechanism of the RalGAP tumor suppressor complex

**Authors:** René Rasche, Björn Udo Klink, Lisa Helene Apken, Esther Michalke, Minghao Chen, Andrea Oeckinghaus, Christos Gatsogiannis, Daniel Kümmel

PMC · DOI: 10.1038/s41467-025-61743-9 · Nature Communications · 2025-07-30

## TL;DR

This paper reveals the structure of the RalGAP tumor suppressor complex, offering insights into how it regulates cancer-related Ras signaling.

## Contribution

The study presents the first cryo-EM structure of the RalGAP complex, elucidating its architecture and functional mechanism.

## Key findings

- RalGAP forms a 58 nm tetrameric structure composed of RalGAPα and RalGAPβ subunits.
- RalGAPβ stabilizes the catalytic domain of RalGAPα, explaining the necessity of heterodimer formation.
- Tetramer formation is essential for in vivo function but not required for in vitro activity.

## 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.

The RalGAP complex is an important tumor suppressor that counteracts oncogenic Ras signaling. Here, Rasche, Klink and colleagues present the cryo-EM structure of RalGAP and provides insight into its mechanism and molecular function.

## Linked entities

- **Genes:** ralgapa1 (Ral GTPase activating protein catalytic subunit alpha 1) [NCBI Gene 100557011], RALGAPB (Ral GTPase activating protein non-catalytic subunit beta) [NCBI Gene 57148], ras (resistance to audiogenic seizures) [NCBI Gene 19412]
- **Proteins:** ralgapa1 (Ral GTPase activating protein catalytic subunit alpha 1), RALGAPB (Ral GTPase activating protein non-catalytic subunit beta), ras (resistance to audiogenic seizures)
- **Diseases:** cancer (MONDO:0004992)

## Full-text entities

- **Genes:** RALB (RAS like proto-oncogene B) [NCBI Gene 5899], RAP1A (RAP1A, member of RAS oncogene family) [NCBI Gene 5906] {aka C21KG, G-22K, KREV-1, KREV1, RAP1, SMGP21}, RAP1GAP (RAP1 GTPase activating protein) [NCBI Gene 5909] {aka RAP1GA1, RAP1GAP1, RAP1GAPII, RAPGAP}, TBK1 (TANK binding kinase 1) [NCBI Gene 29110] {aka AIARV, FTDALS4, IIAE8, NAK, T2K}, MTG1 (mitochondrial ribosome associated GTPase 1) [NCBI Gene 92170] {aka GTP, GTPBP7}, Rala (Ras like proto-oncogene A) [NCBI Gene 56044] {aka 3010001O15Rik, Ral, Rasl1}, EXOC2 (exocyst complex component 2) [NCBI Gene 55770] {aka NEDFACH, SEC5, SEC5L1, Sec5p}, LYZ (lysozyme) [NCBI Gene 4069] {aka AMYLD5, LYZF1, LZM}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, RALGAPA1 (Ral GTPase activating protein catalytic subunit alpha 1) [NCBI Gene 253959] {aka GARNL1, GRIPE, NEDHRIT, RalGAPalpha1, TULIP1, p240}, TBC1D7 (TBC1 domain family member 7) [NCBI Gene 51256] {aka MGCPH, PIG51, TBC7}, TSC2 (TSC complex subunit 2) [NCBI Gene 7249] {aka LAM, PPP1R160, TSC4}, RALGAPB (Ral GTPase activating protein non-catalytic subunit beta) [NCBI Gene 57148] {aka KIAA1219, RalGAPbeta}, YWHAQ (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta) [NCBI Gene 10971] {aka 14-3-3, 1C5, HS1}, LRPAP1 (LDL receptor related protein associated protein 1) [NCBI Gene 4043] {aka A2MRAP, A2RAP, HBP44, MYP23, RAP, alpha-2-MRAP}, RHEB (Ras homolog, mTORC1 binding) [NCBI Gene 6009] {aka RHEB2}, RALBP1 (ralA binding protein 1) [NCBI Gene 10928] {aka RIP1, RLIP1, RLIP76}, RALGAPA2 (Ral GTPase activating protein catalytic subunit alpha 2) [NCBI Gene 57186] {aka AS250, C20orf74, bA287B20.1, dJ1049G11, dJ1049G11.4, p220}, NKIRAS1 (NFKB inhibitor interacting Ras like 1) [NCBI Gene 28512] {aka KBRAS1, kappaB-Ras1}, Rasa1 (RAS p21 protein activator 1) [NCBI Gene 218397] {aka Gap, RasGAP, Rasa}, RALA (RAS like proto-oncogene A) [NCBI Gene 5898] {aka HINCONS, RAL}, TSC1 (TSC complex subunit 1) [NCBI Gene 7248] {aka LAM, TSC}, NKIRAS2 (NFKB inhibitor interacting Ras like 2) [NCBI Gene 28511] {aka KBRAS2, kappaB-Ras2}, EXOC8 (exocyst complex component 8) [NCBI Gene 149371] {aka EXO84, Exo84p, NEDMISB, SEC84}
- **Diseases:** tumorigenesis (MESH:D063646), uterine and skin cancer (MESH:D012878), infantile spasms (MESH:D013036), feeding abnormalities (MESH:D001068), impaired neurodevelopment (MESH:D060825), invasive (MESH:D009361), neonatal respiratory insufficiency (MESH:D012131), tumor suppressor (OMIM:601308), neurodevelopmental disorder (MESH:D002658), hypotonia (MESH:D009123), colitis-associated cancer (MESH:D000083023), oral squamous cell carcinoma (MESH:D000077195), prostate and bladder cancer (MESH:D011471), cancer (MESH:D009369), bladder cancer (MESH:D001749), hepatocellular carcinoma (MESH:D006528), pancreatic cancer (MESH:D010190), PDAC (MESH:D021441), genetic disease (MESH:D030342), metastasis (MESH:D009362)
- **Chemicals:** IPTG (MESH:D007544), TBS-T (MESH:C027647), glucose (MESH:D005947), acetonitrile (MESH:C032159), EDTA (MESH:D004492), UA (MESH:C005460), NaCl (MESH:D012965), Penicillin (MESH:D010406), HEPES (MESH:D006531), Tween (MESH:D011136), puromycin (MESH:D011691), Asn (MESH:D001216), L-Glutamine (MESH:D005973), ALFA (-), phosphoinositides (MESH:D010716), MgCl2 (MESH:D015636), Glycerol (MESH:D005990), DTT (MESH:D004229), T (MESH:D014316), GSH (MESH:D005978), PBS (MESH:D007854), nitrogen (MESH:D009584), NP-40 (MESH:C010615), GDP (MESH:D006153), water (MESH:D014867), Trp (MESH:D014364), CO2 (MESH:D002245), Triton-X100 (MESH:D017830), Streptomycin (MESH:D013307), Agarose (MESH:D012685), TB (MESH:D013725), valproic acid (MESH:D014635), CHAPS (MESH:C028213), SDS (MESH:D012967), ethane (MESH:D004980), TCEP (MESH:C080938), Nucleotide (MESH:D009711), EGTA (MESH:D004533)
- **Species:** Homo sapiens (human, species) [taxon 9606], Sus scrofa (pig, species) [taxon 9823], SV40 [taxon 10633], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** W65R, V37E, W65, 37  C, N1076, V29E, L120C, V33Q, V33, asparagine at position 1742, V37, R1738H
- **Cell lines:** HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), Expi293F — Homo sapiens (Human), Transformed cell line (CVCL_D615), HEK293FT — Homo sapiens (Human), Transformed cell line (CVCL_6911), Escherichia coli BL21 — Homo sapiens (Human), EBV-related Burkitt lymphoma, Cancer cell line (CVCL_M639), MEFs — Mus musculus (Mouse), Finite cell line (CVCL_9115), CVCL_6911 — Mus musculus (Mouse), Embryonic stem cell (CVCL_DR01), C57BL/6 — Mus musculus (Mouse), Transformed cell line (CVCL_C0MU)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12311180/full.md

## References

4 references — full list in the complete paper: https://tomesphere.com/paper/PMC12311180/full.md

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Source: https://tomesphere.com/paper/PMC12311180