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- PDB-9rs9: Rab23 in complex with Fuzzy-Inturned -

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Basic information

Entry
Database: PDB / ID: 9rs9
TitleRab23 in complex with Fuzzy-Inturned
Components
  • Protein fuzzy homolog
  • Protein inturned
  • Ras-related protein Rab-23
KeywordsCYTOSOLIC PROTEIN / longin domain / GEF / nucleotide exchange
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 / craniofacial suture morphogenesis / embryonic body morphogenesis / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / establishment of planar polarity / regulation of cilium assembly ...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 / craniofacial suture 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 / RAB geranylgeranylation / non-motile cilium assembly / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / GTP metabolic process / limb development / neural tube development / motile cilium / embryonic digit morphogenesis / hair follicle morphogenesis / smoothened signaling pathway / negative regulation of protein import into nucleus / roof of mouth development / autophagosome assembly / cilium assembly / regulation of ossification / hair follicle development / negative regulation of keratinocyte proliferation / cellular defense response / Hedgehog 'off' state / keratinocyte differentiation / vesicle-mediated transport / phagocytic vesicle / centriole / endomembrane system / phosphatidylinositol binding / autophagosome / negative regulation of cell migration / small monomeric GTPase / neural tube closure / intracellular protein transport / negative regulation of canonical Wnt signaling pathway / phagocytic vesicle membrane / cell junction / nervous system development / protein transport / cytoskeleton / endosome membrane / ciliary basal body / cilium / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / GTP binding / cell surface / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fuzzy protein / Protein inturned / Ras-related protein Rab-23 / 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 ...Fuzzy protein / Protein inturned / Ras-related protein Rab-23 / 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 / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein fuzzy homolog / Ras-related protein Rab-23 / Protein inturned
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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: To Be Published
Title: Mechanistic Adaptation of the Metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned
Authors: Wilmes, S. / Toenjes, J. / Drechsler, M. / Ruf, A. / Schaefer, J. / Luerick, A. / Januliene, D. / Apelt, S. / Di Iorio, D. / Wegner, S.V. / Loose, M. / Moeller, A. / Paululat, A. / Kuemmel, D.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein fuzzy homolog
B: Protein inturned
C: Ras-related protein Rab-23


Theoretical massNumber of molelcules
Total (without water)180,7083
Polymers180,7083
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
#3: Protein Ras-related protein Rab-23


Mass: 27492.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N121I / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB23, HSPC137 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULC3, small monomeric GTPase
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 with 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60395 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 128.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00337561
ELECTRON MICROSCOPYf_angle_d0.752610251
ELECTRON MICROSCOPYf_chiral_restr0.04271207
ELECTRON MICROSCOPYf_plane_restr0.00391284
ELECTRON MICROSCOPYf_dihedral_angle_d5.31841014

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