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- EMDB-13790: Structure of the mouse CPLANE-RSG1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13790
TitleStructure of the mouse CPLANE-RSG1 complex
Map dataFull Map
Sample
  • Complex: CPLANE complex
    • Protein or peptide: WD repeat-containing and planar cell polarity effector protein fritz homolog
    • Protein or peptide: Protein inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Ciliogenesis and planar polarity effector 2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
Function / homology
Function and homology information


auditory receptor cell morphogenesis / axonemal basal plate / respiratory system development / tongue morphogenesis / regulation of embryonic cell shape / regulation of vesicle fusion / septin cytoskeleton organization / digestive system development / regulation of ruffle assembly / protein localization => GO:0008104 ...auditory receptor cell morphogenesis / axonemal basal plate / respiratory system development / tongue morphogenesis / regulation of embryonic cell shape / regulation of vesicle fusion / septin cytoskeleton organization / digestive system development / regulation of ruffle assembly / protein localization => GO:0008104 / regulation of fibroblast migration / podocyte cell migration / establishment of planar polarity / spinal cord dorsal/ventral patterning / motile cilium assembly / cilium organization / circulatory system development / Hedgehog 'off' state / negative regulation of cell division / positive regulation of cilium assembly / regulation of exocytosis / non-motile cilium assembly / regulation of smoothened signaling pathway / camera-type eye development / positive regulation of smoothened signaling pathway / motile cilium / regulation of establishment of cell polarity / limb development / neural tube development / regulation of focal adhesion assembly / smoothened signaling pathway / embryonic digit morphogenesis / hair follicle morphogenesis / roof of mouth development / exocytosis / axoneme / cilium assembly / regulation of ossification / negative regulation of keratinocyte proliferation / embryonic organ development / vesicle-mediated transport / keratinocyte differentiation / negative regulation of cell migration / ciliary basal body / kidney development / neural tube closure / establishment of protein localization / cilium / regulation of protein localization / protein transport / nervous system development / cytoskeleton / GTPase activity / GTP binding / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Ciliogenesis and planar polarity effector 2 / 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 ...Ciliogenesis and planar polarity effector 2 / 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 / Small GTPase / Ras family / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ciliogenesis and planar polarity effector 2 / Protein fuzzy homolog / Protein inturned / WD repeat-containing and planar cell polarity effector protein fritz homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsLangousis G / Cavadini S / Kempf G / Matthias P
Funding support2 items
OrganizationGrant numberCountry
Swiss National Science Foundation
Other private
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, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateApr 27, 2022-
Current statusApr 27, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13790.png

Downloads & links

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Map

FileDownload / File: emd_13790.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull Map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16326806 - 0.34118095
Average (Standard dev.)-4.0316358e-05 (±0.011359473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened with Locscale

Fileemd_13790_additional_1.map
AnnotationSharpened with Locscale
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_13790_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_13790_half_map_2.map
AnnotationHalf map B
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : CPLANE complex

EntireName: CPLANE complex
Components
  • Complex: CPLANE complex
    • Protein or peptide: WD repeat-containing and planar cell polarity effector protein fritz homolog
    • Protein or peptide: Protein inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Ciliogenesis and planar polarity effector 2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate

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Supramolecule #1: CPLANE complex

SupramoleculeName: CPLANE complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: WD repeat-containing and planar cell polarity effector protein fr...

MacromoleculeName: WD repeat-containing and planar cell polarity effector protein fritz homolog
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 86.286477 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSAVDLEVL FQGPGSFCLT ELHLWSLKST LHIADRDIGV YQYYDKKDPS VSATEHGNL EEKQRLAESR DYPWTLKNRR PEKLRDSLKE LEELMQSSPC VLSKWKSKYI CQLLFGSGVL VSLSLSGPQL E KVVIDRSL ...String:
MDSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSAVDLEVL FQGPGSFCLT ELHLWSLKST LHIADRDIGV YQYYDKKDPS VSATEHGNL EEKQRLAESR DYPWTLKNRR PEKLRDSLKE LEELMQSSPC VLSKWKSKYI CQLLFGSGVL VSLSLSGPQL E KVVIDRSL VGKLISDTIS DALLTDSFII LSFLAQNKLC FIQFTKKMDS LDGNKRLEKL SALDLKISYY DIPGPANRTI DR HLAVNST QDLVVCWWPL VSDDVWPWTP VSSEKDRANM LLLGFTQGGL EVLSFVRTEW SPLDVHFGTK QPYQVFTVEC SVS VDKEPM ADSCIYESVR NKLHCVSVTR IPLRSKAISC CRNSTEDKLI VGCEDSSVIL YEAHRGVTLL AQAELRPSLI SCHP SGAIL LVGSNQGELQ IFDIALSPIN IQLLAEDYSP KETLQFKKFF DVSSSLVQMQ WMAPPVVFQK PKRGEICDLL FLRFN KGPL GVLLFKLGIL TRGQLGLVDL ILQYIHYSEV YEAISILRSM DWDTLGQQCL IGMGTIVNHL LRQRLTPERE AQLEAS LGT FYAPTRPLLD TTILEYREPV SKYARRLFHH LLRYKRFEKA FLLAVDIGAR DLFMDIHYLA LDMGELALAE VARRRAH DI DVESVSSGVE LLGPLDRRDM LNEGFASSAL MPEGENKFPG LLPSIGSTHM QTLQQKIPNG PSSRWAIERR TEEEEEEE E EEEEELCTDS SGATTWNAEG ELKEDQRKQD IGDVGSLRMV HFGLV

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Macromolecule #2: Protein inturned

MacromoleculeName: Protein inturned / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 107.330539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDLEVLFQ GPGAGLARGD SRGRPPELPG DLSSQEEEEE EGDSDAGASS LGSYSSASSD TDVEPEWLDS VQKNGELFY LELSEDEEES LLPETQTANH VNHVRFSDKE VIIEEDDSRE RKKSEPKLRR FTKILKSKSL LPRRHHKKSS S NNGPVSIL ...String:
MGSSHHHHHH SAVDLEVLFQ GPGAGLARGD SRGRPPELPG DLSSQEEEEE EGDSDAGASS LGSYSSASSD TDVEPEWLDS VQKNGELFY LELSEDEEES LLPETQTANH VNHVRFSDKE VIIEEDDSRE RKKSEPKLRR FTKILKSKSL LPRRHHKKSS S NNGPVSIL KHQSSQKTGV TVQQRYKDVT VYINPRKLTA IKAREQVKLL EVLVGIIHQT KRSWKRSAKQ ADGERLVVHG LL PGGSAMK SGQVLVGDVL VAVNDVDVTS ENIERVLSCI PGPMQVKLTF ENAYAVKRET AQPQKKKAQS STQDLVKLLC GSE ADAVQH STLSIPHISM YLTLQLQSEA AREEQEILYH YPVSEASQKL KSVRGIFLTL CDMLESVTGT QVTSSSLHLN GKQI HVAYL KESDKLLLIG LPAEEVPLPQ LRNMIEDVAQ TLKFMYGSLD SAFCQVENAP RLDHFFSLFF ERALRPGKLH LSGSP SAQQ YAAASAVLLD NLPGVRWLVL PQELKVELDT ALSDLEAADF EELSEDYYDM RRLYTILGSS LFYKGYMVCS HLPKDD VIE IAAYCRQHCL LPLAAKQRIG QLIIWREVFP RHHLQPPSDS DPEAFQEPEG RYFLLVVGLR HYLLCVLLEA GGCASKA TG NPGPDCIYVD QVRATLHQLE GVDSRIEEQL ATSPGPCLSC ADWFLAAPRE KADSLTTSPI LSRLQGPSKT AASPTCRR T FFSDYSFKAR KPSPSRIGGG REPTEGEESA GLSPHATPDA VRKQRESEGS DDNVALLKLA RKKSTLPNPF HLGTSKKEL SEKELEVYDI MKLTSGPENT LFHYVALETV QGIFITPTHE EVAQLGGSVH SQLIKNFHQC CLSIRAFFQQ TLKEEKKKAL SDGEHSEPT NSVSSLSPVK EHGVLFECSP ENWTDQKKTP PVMSYWVVGR LFLNPKPQEL YVCFHDSVSE IAIEMAFKLF F GLTL

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Macromolecule #3: Protein fuzzy homolog

MacromoleculeName: Protein fuzzy homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 45.542906 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDEGPGSPVH LLCLAASSGV PLFCRSSSGG APSRQQLPFS VIGSLNGVHM FGQNLDVQLN SARTEDTTVV WKNFHDSITL IVLSSEEGT SELRLERMLH MVFGAMVLIV GLEELTNIRN VERLKKELRA SYCLIDSFLG NSELIGDLTQ CVDCVIPPEG S AMQETLSG ...String:
MDEGPGSPVH LLCLAASSGV PLFCRSSSGG APSRQQLPFS VIGSLNGVHM FGQNLDVQLN SARTEDTTVV WKNFHDSITL IVLSSEEGT SELRLERMLH MVFGAMVLIV GLEELTNIRN VERLKKELRA SYCLIDSFLG NSELIGDLTQ CVDCVIPPEG S AMQETLSG FAEATGTAFV SLLVSGRVVA ATEGWWRLGM PEAVLLPWLV GSLPPQAARD YPVYLPHGSP TVPHRLLTLT LL RGLELCL LCGPRPPLGQ LDPQLMERWW QPLLEPLRAC LPLGPRALPE GFPLHSDILG LLLLHLELRR CLFTVEPSKD KEP SPEQRR RLLRNFYTLV ATTHFPPEPG PAEKQEDTVY PAQMPRACYL VLGPGMGWQL VAVQLGLRLL LLLLSPHTPT HGLR SLATR TLQALTPLL

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Macromolecule #4: Ciliogenesis and planar polarity effector 2

MacromoleculeName: Ciliogenesis and planar polarity effector 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.459801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARPPMHGSV IVPDWHETVE GKEYLACILR KNRRREFGLL ERPVLPPSVV IDTASYKIFV SGKSGVGKTA LVAKLAGLEV PIVHHETTG IQTTVVFWPA KLKASDCVVM FRFEFWDCGE SALKKFDHML PACKENADAF LFLFSFTDRA SFEDLPGQLT R VAGEAPGL ...String:
MARPPMHGSV IVPDWHETVE GKEYLACILR KNRRREFGLL ERPVLPPSVV IDTASYKIFV SGKSGVGKTA LVAKLAGLEV PIVHHETTG IQTTVVFWPA KLKASDCVVM FRFEFWDCGE SALKKFDHML PACKENADAF LFLFSFTDRA SFEDLPGQLT R VAGEAPGL VKIVIGSKFD QYMHTDVPAR DLTAFRQAWE LPLFRVKSVP GRRLADGRTL DGRAGLADTA HVLNGLAEQL WH QDQVAAG LLPSSPESAP G

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.04 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94157

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