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- EMDB-60540: the Planar Cell Polarity Core Protein Vangl1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60540
Titlethe Planar Cell Polarity Core Protein Vangl1
Map data
Sample
  • Complex: Vang-like protein 1
    • Protein or peptide: Vang-like protein 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
KeywordsNTD / PCP / Vangl / Prickle / STRUCTURAL PROTEIN
Function / homology
Function and homology information


mucociliary clearance / RHOD GTPase cycle / RHOF GTPase cycle / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / RND3 GTPase cycle / RHOV GTPase cycle / RHOB GTPase cycle / pigmentation ...mucociliary clearance / RHOD GTPase cycle / RHOF GTPase cycle / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / RND3 GTPase cycle / RHOV GTPase cycle / RHOB GTPase cycle / pigmentation / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / lateral plasma membrane / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / extracellular region / plasma membrane
Similarity search - Function
Vang-like protein / Strabismus protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang F / Chen S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82101213 China
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure and oligomerization of the human planar cell polarity core protein Vangl1.
Authors: Fan Zhang / Shaobai Li / Hao Wu / Shanshuang Chen /
Abstract: Vangl is a planar cell polarity (PCP) core protein essential for aligned cell orientation along the epithelial plane perpendicular to the apical-basal direction, which is important for tissue ...Vangl is a planar cell polarity (PCP) core protein essential for aligned cell orientation along the epithelial plane perpendicular to the apical-basal direction, which is important for tissue morphogenesis, development and collective cell behavior. Mutations in Vangl are associated with developmental defects, including neural tube defects (NTDs), according to human cohort studies of sporadic and familial cases. The complex mechanisms underlying Vangl-mediated PCP signaling or Vangl-associated human congenital diseases have been hampered by the lack of molecular characterizations of Vangl. Here, we show biochemical and structural evidence that human Vangl1 oligomerizes as dimers of trimers, and that the dimerization of trimers promotes binding to the PCP effector Prickle1 (Pk1) in vitro. Mapping of human disease-associated point mutations suggests potential pathological mechanisms and paves the way for future studies on the importance of lipid binding, central vestibule and oligomerization of Vangl, thereby providing insights into the molecular mechanisms of the PCP signaling pathway.
History
DepositionJun 14, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60540.png

Downloads & links

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Map

FileDownload / File: emd_60540.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.206
Minimum - Maximum-1.1802546 - 2.2171571
Average (Standard dev.)0.0009078518 (±0.03478771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60540_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60540_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Vang-like protein 1

EntireName: Vang-like protein 1
Components
  • Complex: Vang-like protein 1
    • Protein or peptide: Vang-like protein 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Vang-like protein 1

SupramoleculeName: Vang-like protein 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vang-like protein 1

MacromoleculeName: Vang-like protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.053887 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTESTYSGY SYYSSHSKKS HRQGERTRER HKSPRNKDGR GSEKSVTIQP PTGEPLLGND STRTEEVQDD NWGETTTAIT GTSEHSISQ EDIARISKDM EDSVGLDCKR YLGLTVASFL GLLVFLTPIA FILLPPILWR DELEPCGTIC EGLFISMAFK L LILLIGTW ...String:
MDTESTYSGY SYYSSHSKKS HRQGERTRER HKSPRNKDGR GSEKSVTIQP PTGEPLLGND STRTEEVQDD NWGETTTAIT GTSEHSISQ EDIARISKDM EDSVGLDCKR YLGLTVASFL GLLVFLTPIA FILLPPILWR DELEPCGTIC EGLFISMAFK L LILLIGTW ALFFRKRRAD MPRVFVFRAL LLVLIFLFVV SYWLFYGVRI LDSRDRNYQG IVQYAVSLVD ALLFIHYLAI VL LELRQLQ PMFTLQVVRS TDGESRFYSL GHLSIQRAAL VVLENYYKDF TIYNPNLLTA SKFRAAKHMA GLKVYNVDGP SNN ATGQSR AMIAAAARRR DSSHNELYYE EAEHERRVKK RKARLVVAVE EAFIHIQRLQ AEEQQKAPGE VMDPREAAQA IFPS MARAL QKYLRITRQQ NYHSMESILQ HLAFCITNGM TPKAFLERYL SAGPTLQYDK DRWLSTQWRL VSDEAVTNGL RDGIV FVLK CLDFSLVVNV KKIPFIILSE EFIDPKSHKF VLRLQSETSV

UniProtKB: Vang-like protein 1

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 6 / Formula: MC3
Molecular weightTheoretical: 677.933 Da
Chemical component information

ChemComp-MC3:
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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

Concentration8 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 718127
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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