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- PDB-7q3d: Structure of the human CPLANE complex -

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Basic information

Entry
Database: PDB / ID: 7q3d
TitleStructure of the human CPLANE complex
Components
  • Protein fuzzy homolog
  • Protein inturned
  • WD repeat-containing and planar cell polarity effector protein fritz homolog
KeywordsPROTEIN TRANSPORT / ciliogenesis / ciliopathies / longin / lipid binding
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 / axonemal basal plate / respiratory system development / tongue morphogenesis / auditory receptor cell morphogenesis / regulation of embryonic cell shape / septin cytoskeleton organization / digestive system development / embryonic body morphogenesis ...negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / axonemal basal plate / respiratory system development / tongue morphogenesis / auditory receptor cell morphogenesis / regulation of embryonic cell shape / septin cytoskeleton organization / digestive system development / embryonic body morphogenesis / regulation of ruffle assembly / regulation of fibroblast migration / podocyte cell migration / establishment of planar polarity / protein localization to organelle / intraciliary transport / spinal cord dorsal/ventral patterning / ciliary transition zone / regulation of cilium assembly / motile cilium assembly / embryonic skeletal system morphogenesis / cilium organization / negative regulation of cell division / circulatory system development / positive regulation of cilium assembly / non-motile cilium assembly / camera-type eye development / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / motile cilium / limb development / neural tube development / regulation of establishment of cell polarity / regulation of focal adhesion assembly / embryonic digit morphogenesis / hair follicle morphogenesis / smoothened signaling pathway / roof of mouth development / axoneme / hair follicle development / cilium assembly / regulation of ossification / negative regulation of keratinocyte proliferation / Hedgehog 'off' state / vesicle-mediated transport / keratinocyte differentiation / centriole / phosphatidylinositol binding / ciliary basal body / negative regulation of cell migration / kidney development / neural tube closure / establishment of protein localization / negative regulation of canonical Wnt signaling pathway / cilium / protein transport / regulation of protein localization / nervous system development / cytoskeleton / negative regulation of cell population proliferation / cell division / cell surface / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
WD repeat-containing and planar cell polarity effector protein Fritz / Fuzzy protein / Protein inturned / WD repeat-containing and planar cell polarity effector protein Fritz / 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 ...WD repeat-containing and planar cell polarity effector protein Fritz / Fuzzy protein / Protein inturned / WD repeat-containing and planar cell polarity effector protein Fritz / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing and planar cell polarity effector protein fritz homolog / Protein fuzzy homolog / Protein inturned
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsLangousis, G. / Cavadini, S. / Kempf, G. / Matthias, P.
Funding support1items
OrganizationGrant numberCountry
Swiss National Science Foundation
CitationJournal: Sci Adv / Year: 2022
Title: Structure of the ciliogenesis-associated CPLANE complex.
Authors: Gerasimos Langousis / Simone Cavadini / Niels Boegholm / Esben Lorentzen / Georg Kempf / Patrick Matthias /
Abstract: Dysfunctional cilia cause pleiotropic human diseases termed ciliopathies. These hereditary maladies are often caused by defects in cilia assembly, a complex event that is regulated by the ...Dysfunctional cilia cause pleiotropic human diseases termed ciliopathies. These hereditary maladies are often caused by defects in cilia assembly, a complex event that is regulated by the ciliogenesis and planar polarity effector (CPLANE) proteins Wdpcp, Inturned, and Fuzzy. CPLANE proteins are essential for building the cilium and are mutated in multiple ciliopathies, yet their structure and molecular functions remain elusive. Here, we show that mammalian CPLANE proteins comprise a bona fide complex and report the near-atomic resolution structures of the human Wdpcp-Inturned-Fuzzy complex and of the mouse Wdpcp-Inturned-Fuzzy complex bound to the small guanosine triphosphatase Rsg1. Notably, the crescent-shaped CPLANE complex binds phospholipids such as phosphatidylinositol 3-phosphate via multiple modules and a CPLANE ciliopathy mutant exhibits aberrant lipid binding. Our study provides critical structural and functional insights into an enigmatic ciliogenesis-associated complex as well as unexpected molecular rationales for ciliopathies.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing and planar cell polarity effector protein fritz homolog
B: Protein inturned
C: Protein fuzzy homolog


Theoretical massNumber of molelcules
Total (without water)243,5223
Polymers243,5223
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10090 Å2
ΔGint-59 kcal/mol
Surface area54940 Å2

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Components

#1: Protein WD repeat-containing and planar cell polarity effector protein fritz homolog / hFRTZ / Bardet-Biedl syndrome 15 protein / WD repeat-containing and planar cell polarity effector protein


Mass: 89649.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDPCP, BBS15, C2orf86, FRITZ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95876
#2: Protein Protein inturned / Inturned planar cell polarity effector homolog / PDZ domain-containing protein 6


Mass: 108150.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTU, KIAA1284, PDZD6, PDZK6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULD6
#3: Protein Protein fuzzy homolog


Mass: 45721.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUZ, FY / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BT04

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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: CPLANE / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.04 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
8ISOLDEmodel fitting
9PHENIXmodel fitting
15Rosettamodel refinement
16ISOLDEmodel refinement
17PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129902 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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