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- PDB-9rs8: human Fuzzy-Inturned -

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Basic information

Entry
Database: PDB / ID: 9rs8
Titlehuman Fuzzy-Inturned
Components
  • Protein fuzzy homolog
  • Protein inturned
KeywordsCYTOSOLIC PROTEIN / longin domain / GEF / nucleotide exchange / endosome / autophagosome
Function / homology
Function and homology information


negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly / ciliary transition zone ...negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly / ciliary transition zone / motile cilium assembly / embryonic skeletal system morphogenesis / negative regulation of cell division / positive regulation of cilium assembly / non-motile cilium assembly / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / limb development / neural tube development / motile cilium / embryonic digit morphogenesis / hair follicle morphogenesis / smoothened signaling pathway / roof of mouth development / regulation of ossification / cilium assembly / hair follicle development / negative regulation of keratinocyte proliferation / Hedgehog 'off' state / keratinocyte differentiation / vesicle-mediated transport / centriole / phosphatidylinositol binding / negative regulation of cell migration / neural tube closure / negative regulation of canonical Wnt signaling pathway / nervous system development / protein transport / cytoskeleton / cilium / ciliary basal body / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / cell surface / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Fuzzy protein / Protein inturned / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain ...Fuzzy protein / Protein inturned / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Protein fuzzy homolog / Protein inturned
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWilmes, S. / Schaefer, J. / Januliene, D. / Moeller, A. / Kuemmel, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557-P10 Germany
German Research Foundation (DFG)SFB1557-P11 Germany
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.
Authors: Stephan Wilmes / Jesse Tönjes / Maik Drechsler / Anita Ruf / Jan-Hannes Schäfer / Anna Lürick / Dovile Januliene / Steven Apelt / Daniele Di Iorio / Seraphine V Wegner / Martin Loose / ...Authors: Stephan Wilmes / Jesse Tönjes / Maik Drechsler / Anita Ruf / Jan-Hannes Schäfer / Anna Lürick / Dovile Januliene / Steven Apelt / Daniele Di Iorio / Seraphine V Wegner / Martin Loose / Arne Moeller / Achim Paululat / Daniel Kümmel /
Abstract: Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure ...Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure fidelity. Our structural and functional comparison of the tri-longin domain RabGEFs Mon1-Ccz1 and Fuzzy-Inturned reveals the molecular basis for their target specificity. Both complexes rely on a conserved sequence motif of their substrate GTPases for the catalytic mechanism, while secondary interactions allow discrimination between targets. We also find that dimeric Mon1-Ccz1 from fungi and the metazoan homologs with the additional third subunit RMC1/Bulli bind membranes through electrostatic interactions via distinct interfaces. Protein-lipid interaction studies and functional characterization in flies reveal an essential function of RMC1/Bulli as mediator of GEF complex membrane recruitment. In the case of Fuzzy-Inturned, reconstitution experiments demonstrate that the BAR (Bin-Amphiphysin-Rvs) domain protein CiBAR1 can support membrane recruitment of the GEF. Collectively, our study demonstrates the molecular basis for the adaptation of TLD-RabGEFs to different cellular functions.
History
DepositionJun 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fuzzy homolog
B: Protein inturned


Theoretical massNumber of molelcules
Total (without water)153,2162
Polymers153,2162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein fuzzy homolog


Mass: 45689.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUZ, FY / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BT04
#2: Protein Protein inturned / Inturned planar cell polarity effector homolog / PDZ domain-containing protein 6


Mass: 107526.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTU, KIAA1284, PDZD6, PDZK6 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULD6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human Rab23 GEF Fuzzy-Inturned / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.3
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37728 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 146.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00356196
ELECTRON MICROSCOPYf_angle_d0.75598421
ELECTRON MICROSCOPYf_chiral_restr0.0427999
ELECTRON MICROSCOPYf_plane_restr0.00351052
ELECTRON MICROSCOPYf_dihedral_angle_d4.8616822

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