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- EMDB-13789: Structure of the human CPLANE complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13789
TitleStructure of the human CPLANE complex
Map dataFull map
Sample
  • Complex: CPLANE
    • 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
Keywordsciliogenesis / ciliopathies / longin / lipid binding / PROTEIN TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsLangousis G / Cavadini S
Funding support1 items
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, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13789.png

Downloads & links

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Map

FileDownload / File: emd_13789.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 380 pix.
= 250.8 Å		0.66 Å/pix.
x 380 pix.
= 250.8 Å		0.66 Å/pix.
x 380 pix.
= 250.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.46606022 - 1.0097167
Average (Standard dev.)-0.002717645 (±0.036749214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 250.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Locally sharpened map

Fileemd_13789_additional_1.map
AnnotationLocally sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_13789_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_13789_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CPLANE

EntireName: CPLANE
Components
  • Complex: CPLANE
    • 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

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Supramolecule #1: CPLANE

SupramoleculeName: CPLANE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 89.64932 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSAVDLEVL FQGPGRREFC WDAYSKAAGS RASSPLPRQD RDSFCHQMSF CLTELHLWS LKNTLHIADR DIGIYQYYDK KDPPATEHGN LEKKQKLAES RDYPWTLKNR RPEKLRDSLK ELEELMQNSR C VLSKWKNK ...String:
MDSAWSHPQF EKGGGSGGGS GGSAWSHPQF EKSAVDLEVL FQGPGRREFC WDAYSKAAGS RASSPLPRQD RDSFCHQMSF CLTELHLWS LKNTLHIADR DIGIYQYYDK KDPPATEHGN LEKKQKLAES RDYPWTLKNR RPEKLRDSLK ELEELMQNSR C VLSKWKNK YVCQLLFGSG VLVSLSLSGP QLEKVVIDRS LVGKLISDTI SDALLTDSFI ILSFLAQNKL CFIQFTKKME SS DVNKRLE KLSALDYKIF YYEIPGPINK TTERHLAINC VHDRVVCWWP LVNDDAWPWA PISSEKDRAN LLLLGYAQGR LEV LSSVRT EWDPLDVRFG TKQPYQVFTV EHSVSVDKEP MADSCIYECI RNKIQCVSVT RIPLKSKAIS CCRNVTEDKL ILGC EDSSL ILYETHRRVT LLAQTELLPS LISCHPSGAI LLVGSNQGEL QIFDMALSPI NIQLLAEDRL PRETLQFSKL FDASS SLVQ MQWIAPQVVS QKGEGSDIYD LLFLRFERGP LGVLLFKLGV FTRGQLGLID IIFQYIHCDE IYEAINILSS MNWDTL GHQ CFISMSAIVN HLLRQKLTPE REAQLETSLG TFYAPTRPLL DSTILEYRDQ ISKYARRFFH HLLRYQRFEK AFLLAVD VG ARDLFMDIHY LALDKGELAL AEVARKRASD IDAESITSGV ELLGPLDRGD MLNEAFIGLS LAPQGEDSFP DNLPPSCP T HRHILQQRIL NGSSNRQIID RRNELEKDIC SGFLMTNTCN AEDGELREDG REQEIRDGGS LKMIHFGLV

UniProtKB: WD repeat-containing and planar cell polarity effector protein fritz homolog

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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: Homo sapiens (human)
Molecular weightTheoretical: 108.150633 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDLEVLFQ GPGASVASCD SRPSSDELPG DPSSQEEDED YDFEDRVSDS GSYSSASSDY DDLEPEWLDS VQKNGELFY LELSEDEEES LLPETPTVNH VRFSENEIII EDDYKERKKY EPKLKQFTKI LRRKRLLPKR CNKKNSNDNG P VSILKHQS ...String:
MGSSHHHHHH SAVDLEVLFQ GPGASVASCD SRPSSDELPG DPSSQEEDED YDFEDRVSDS GSYSSASSDY DDLEPEWLDS VQKNGELFY LELSEDEEES LLPETPTVNH VRFSENEIII EDDYKERKKY EPKLKQFTKI LRRKRLLPKR CNKKNSNDNG P VSILKHQS NQKTGVIVQQ RYKDVNVYVN PKKLTVIKAK EQLKLLEVLV GIIHQTKWSW RRTGKQGDGE RLVVHGLLPG GS AMKSGQV LIGDVLVAVN DVDVTTENIE RVLSCIPGPM QVKLTFENAY DVKRETSHPR QKKTQSNTSD LVKLLWGEEV EGI QQSGLN TPHIIMYLTL QLDSETSKEE QEILYHYPMS EASQKLKSVR GIFLTLCDML ENVTGTQVTS SSLLLNGKQI HVAY WKESD KLLLIGLPAE EVPLPRLRNM IENVIQTLKF MYGSLDSAFC QIENVPRLDH FFNLFFQRAL QPAKLHSSAS PSAQQ YDAS SAVLLDNLPG VRWLTLPLEI KMELDMALSD LEAADFAELS EDYYDMRRLY TILGSSLFYK GYLICSHLPK DDLIDI AVY CRHYCLLPLA AKQRIGQLII WREVFPQHHL RPLADSSTEV FPEPEGRYFL LVVGLKHYML CVLLEAGGCA SKAIGSP GP DCVYVDQVKT TLHQLDGVDS RIDERLASSP VPCLSCADWF LTGSREKTDS LTTSPILSRL QGTSKVATSP TCRRTLFG D YSLKTRKPSP SCSSGGSDNG CEGGEDDGFS PHTTPDAVRK QRESQGSDGL EESGTLLKVT KKKSTLPNPF HLGNLKKDL PEKELEIYNT VKLTSGPENT LFHYVALETV QGIFITPTLE EVAQLSGSIH PQLIKNFHQC CLSIRAVFQQ TLVEEKKKGL NSGDHSDSA KSVSSLNPVK EHGVLFECSP GNWTDQKKAP PVMAYWVVGR LFLHPKPQEL YVCFHDSVTE IAIEIAFKLF F GLTL

UniProtKB: Protein inturned

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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: Homo sapiens (human)
Molecular weightTheoretical: 45.721949 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS ...String:
MGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS GFAEAAGTTF VSLVVSGRVV AATEGWWRLG TPEAVLLPWL VGSLPPQTAR DYPVYLPHGS PTVPHRLLTL TL LPSLELC LLCGPSPPLS QLYPQLLERW WQPLLDPLRA CLPLGPRALP SGFPLHTDIL GLLLLHLELK RCLFTVEPLG DKE PSPEQR RRLLRNFYTL VTSTHFPPEP GPPEKTEDEV YQAQLPRACY LVLGTEEPGT GVRLVALQLG LRRLLLLLSP QSPT HGLRS LATHTLHALT PLL

UniProtKB: Protein fuzzy homolog

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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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.04 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129902
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7q3d:
Structure of the human CPLANE complex

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