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Structure of Rab11–FIP3–Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11

Nature Structural & Molecular Biology volume 22, pages 695–702 (2015)Cite this article

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Abstract

The small GTPase Rab11 and its effectors FIP3 and Rabin8 are essential to membrane-trafficking pathways required for cytokinesis and ciliogenesis. Although effector binding is generally assumed to be sequential and mutually exclusive, we show that Rab11 can simultaneously bind FIP3 and Rabin8. We determined crystal structures of human Rab11–GMPPNP–Rabin8 and Rab11–GMPPNP–FIP3–Rabin8. The structures reveal that the C-terminal domain of Rabin8 adopts a previously undescribed fold that interacts with Rab11 at an unusual effector-binding site neighboring the canonical FIP3-binding site. We show that Rab11–GMPPNP–FIP3–Rabin8 is more stable than Rab11–GMPPNP–Rabin8, owing to direct interaction between Rabin8 and FIP3 within the dual effector–bound complex. The data allow us to propose a model for how membrane-targeting complexes assemble at the trans-Golgi network and recycling endosomes, through multiple weak interactions that create high-avidity complexes.

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Figure 1: Crystal structure of heterotetrameric Rab11–Rabin8C.
Figure 2: Simultaneous binding of Rabin8 and FIP3 effectors to Rab11.
Figure 3: Crystal structure of Rab11–FIP3–Rabin8.
Figure 4: Rab11–FIP3–Rabin8 exists in a concentration-dependent equilibrium between different oligomeric states.
Figure 5: Model of the ciliary-targeting complex at the donor membrane.

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Acknowledgements

We thank the staff at the Swiss Light Source for assistance with X-ray diffraction data collection and the crystallization facility and microchemistry core facility at the Max Planck Institute of Biochemistry for access to crystallization screening and ultracentrifugation, respectively. We acknowledge the facility at the Department of Chemistry at the Technical University Munich for SAXS measurements (German Research Council (DFG), grant SFB1035) and M. Morawetz and M. Stiegler for technical assistance with molecular biology. We also thank M. Taschner for making the schematics in Figure 5b. This work was funded by an Emmy Noether grant (DFG grant LO1627/1-1), by the European Research Council (ERC starter grant 310343) and by the European Molecular Biology Organization Young Investigator Program.

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Authors and Affiliations

  1. Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Melanie Vetter, Claire Basquin & Esben Lorentzen

  2. Department of Chemistry, Technical University Munich, Munich, Germany

    Ralf Stehle

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  1. Melanie Vetter
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  2. Ralf Stehle
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Contributions

M.V. carried out the protein biochemistry and structural biology under the supervision of E.L. R.S. carried out the SAXS measurements and calculations. C.B. assisted with the ITC measurements. E.L. and M.V. wrote the paper with input from R.S. and C.B.

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Correspondence to Esben Lorentzen.

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Integrated supplementary information

Supplementary Figure 1 Size-exclusion chromatography (SEC), ultracentrifugation and interface validation of Rab11–Rabin8C.

(a) (left) SEC elution profile for Rabin8C (orange), Rab11 (blue) and a stoichiometric mixture of Rab11-Rabin8C incubated for 1h prior to loading onto a superdex 200 column. (right) SDS PAGE of the peak fractions from the Rab11-Rabin8C elution. Both the elution profile and the SDS-PAGE gel show that a stable Rab11-Rabin8C complex is not formed during the chromatography step. (b) Sedimentation velocity ultracentrifugation experiments for Rabin8C (left) and the Rab11-FIP3RBD complex (right). The determined Mw of Rabin8C was 41kDa, which corresponds to a homo-dimer (Mwcalc=44kDa) and is consistent with our crystallographic data. The determined Mw for the Rab11-FIP3RBD complex was 56kDa consistent with a hetero-tetramer containing two copies of each protein (Mwcalc=56kDa). This result is consistent with the crystallographic data previously published. (c) Ni-NTA pull-down of constitutively active Rab11(Q70L) using Wild-type (WT) and five different Rab11-interface single point-mutants (mut) of His-tagged Rabin8C. None of the mutations abolish Rab11-Rabin8C complex formation. (d) SEC profile of WT and triple-mutant Rabin8C (T419, Y423, L428 to alanine) demonstrating that the mutant Rabin8C elutes in a similarly peak to WT Rabin8C and is thus folded. (e) Ni-NTA pull-down of constitutively active Rab11(Q70L) using WT and the Rab11-interface triple point-mutant of His-tagged Rabin8C. The triple mutation substantially reduces complex formation with Rab11. An asterisk marks a band on the SDS-gel that corresponds to Rabin8C with the HIS-tagged cleaved. The cleaved form of Rabin8C nevertheless binds to Ni-NTA resin under PBS pH 7.5 and 10mM imidazole conditions and is pulled down similarly to HIS-tagged Rabin8C.

Supplementary Figure 2 Topology of the Rabin8C domain.

Searches using the DALI server (Holm, L & Rosenström et al., Nucleic Acids Research. 38, W545–9, 2010) with the Rabin8C structure did not reveal any previously determined structure of the same fold. The diagram on the left shows the topology of one Rabin8C monomer in orange with the domain-swapped beta-strands of the neighboring subunit in the homo-dimer shown in yellow. The topology diagram was generated using Pro-origami (Stivala, A. et al., Bioinformatics. 27, 3315–3316, 2011). The right panel shows the Rabin8C dimer structure. The two subunits are interlinked via the domain-swapped beta-strands to resemble a single pair of crab claws and we thus designate the Rabin8C fold the Crab-fold.

Supplementary Figure 3 Structural overlay of Rab11–Rabin8C with Rab11–PI4KIIIβ, structural model for Rab11–FIP3–Rabin8C and interactions of ciliary-targeting-complex subunits.

(a) Superpositioning of Rab11-Rabin8C and Rab11-PI4KIIIb (PDB code: 4D0L) structures reveal that Rabin8 and PI4KIIIb use similar binding sites on Rab11 despite adopting different folds. (b) Modeled dodecameric Rab11-FIP3-Rabin8 complex based on the structural superpositioning of Rab11-FIP3 (PDB code 2HV8) and Rab11-Rabin8 crystal structures. The model shows a closed arrangement of the complex with no unpaired dimerization interfaces. Several clashes, indicated by a red box, occur between FIP3 and Rabin8 at the center of the model suggesting that conformational rearrangements have to take place to accommodate a dodecameric structure. (c) Ni-NTA pull-downs of FIP3 and Rab11 with His-tagged Rabin8 demonstrates the formation of dual-effector-bound Rab11 complexes with full-length Rab11, FIP3 and Rabin8 constructs. Rabin8fl is prone to degradation from the N-termini giving rise to a pronounced smear of truncated Rabin8 proteins in the gel.

Supplementary Figure 4 Packing of Rab11–FIP3–Rabin8C complexes in the crystals.

(a) Crystal packing for the 3.0Å P21 data reveals oligomerization of Rab11- FIP3RBD-Rabin8C dodecamers via the well-characterized FIP3RBD homo-dimerization interface. (b) Structure of dodecameric Rab11-FIP3RBD-Rabin8C as found in the asymmetric unit of the crystals. In this structure, two central FIP3RBD helices dimerize to form an asymmetric dodecamer with close contacts to only one of the two Rabin8C dimers. The contacts between the central FIP3RBD homo-dimer and the 1st Rabin8C homo-dimer induce a rotation that results in close interactions of the 3rd and 4th Rab11 molecule. This in turn exposes one FIP3RBD helix at each side of the dodecamer as shown in the perpendicular view.

Supplementary Figure 5 Structural comparison with Rab6–GCC185.

Structural overlay of the Rab6-GCC185RBD complex structure (PDB code 3BBP) onto the Rab11-FIP3RBD hetero-tetramer of the Rab11-FIP3RBD-Rabin8C dodecameric structure presented here. The two structures superimpose well with an RMSD of 3Å. The binding site of Rabin8 on Rab11 is unoccupied in the Rab6-GCC185 structure.

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Vetter, M., Stehle, R., Basquin, C. et al. Structure of Rab11–FIP3–Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11. Nat Struct Mol Biol 22, 695–702 (2015). https://doi.org/10.1038/nsmb.3065

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