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- EMDB-61546: Human VANGL2 hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-61546
TitleHuman VANGL2 hexamer
Map data
Sample
  • Complex: VANGL2 hexamer
    • Protein or peptide: Vang-like protein 2
KeywordsVANGL / Planar cell polarity / PCP / MEMBRANE PROTEIN
Function / homology
Function and homology information


cell migration involved in kidney development / dopaminergic neuron axon guidance / serotonergic neuron axon guidance / establishment of planar polarity / non-motile cilium assembly / apical protein localization / PCP/CE pathway / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle ...cell migration involved in kidney development / dopaminergic neuron axon guidance / serotonergic neuron axon guidance / establishment of planar polarity / non-motile cilium assembly / apical protein localization / PCP/CE pathway / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / RND3 GTPase cycle / heart looping / lateral plasma membrane / Asymmetric localization of PCP proteins / neural tube closure / postsynaptic density membrane / cell-cell junction / apical plasma membrane / glutamatergic synapse / 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
AuthorsSong Y / Zhang Z / Jian S / Zheng P
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)YFA1302300 China
National Natural Science Foundation of China (NSFC)32171201 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of human VANGL-PRICKLE interaction.
Authors: Yanyi Song / Shuyi Jian / Junlin Teng / Pengli Zheng / Zhe Zhang /
Abstract: Planar cell polarity (PCP) is an evolutionarily conserved process for development and morphogenesis in metazoans. The well-organized polarity pattern in cells is established by the asymmetric ...Planar cell polarity (PCP) is an evolutionarily conserved process for development and morphogenesis in metazoans. The well-organized polarity pattern in cells is established by the asymmetric distribution of two core protein complexes on opposite sides of the cell membrane. The Van Gogh-like (VANGL)-PRICKLE (PK) pair is one of these two key regulators; however, their structural information and detailed functions have been unclear. Here, we present five cryo-electron microscopy structures of human VANGL1, VANGL2, and their complexes with PK1 at resolutions of 2.2-3.0 Å. Through biochemical and cell imaging experiments, we decipher the molecular details of the VANGL-PK interaction. Furthermore, we reveal that PK1 can target VANGL-containing intracellular vesicles to the peripheral cell membrane. These findings provide a solid foundation to understand the explicit interaction between VANGL and PK while opening new avenues for subsequent studies of the PCP pathway.
History
DepositionSep 15, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61546.png

Downloads & links

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Map

FileDownload / File: emd_61546.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.526567 - 2.3502972
Average (Standard dev.)-0.00006317864 (±0.03670456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map refined with C3 symmetry

Fileemd_61546_additional_1.map
AnnotationUnsharpened map refined with C3 symmetry
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_61546_half_map_1.map
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Half map: #1

Fileemd_61546_half_map_2.map
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Sample components

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Entire : VANGL2 hexamer

EntireName: VANGL2 hexamer
Components
  • Complex: VANGL2 hexamer
    • Protein or peptide: Vang-like protein 2

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Supramolecule #1: VANGL2 hexamer

SupramoleculeName: VANGL2 hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Vang-like protein 2

MacromoleculeName: Vang-like protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.374074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPSRATMDTE SQYSGYSYKS GHSRSSRKHR DRRDRHRSKS RDGGRGDKSV TIQAPGEPLL DNESTRGDER DDNWGETTTV VTGTSEHSI SHDDLTRIAK DMEDSVPLDC SRHLGVAAGA TLALLSFLTP LAFLLLPPLL WREELEPCGT ACEGLFISVA F KLLILLLG ...String:
GPSRATMDTE SQYSGYSYKS GHSRSSRKHR DRRDRHRSKS RDGGRGDKSV TIQAPGEPLL DNESTRGDER DDNWGETTTV VTGTSEHSI SHDDLTRIAK DMEDSVPLDC SRHLGVAAGA TLALLSFLTP LAFLLLPPLL WREELEPCGT ACEGLFISVA F KLLILLLG SWALFFRRPK ASLPRVFVLR ALLMVLVFLL VVSYWLFYGV RILDARERSY QGVVQFAVSL VDALLFVHYL AV VLLELRQ LQPQFTLKVV RSTDGASRFY NVGHLSIQRV AVWILEKYYH DFPVYNPALL NLPKSVLAKK VSGFKVYSLG EEN STNNST GQSRAVIAAA ARRRDNSHNE YYYEEAEHER RVRKRRARLV VAVEEAFTHI KRLQEEEQKN PREVMDPREA AQAI FASMA RAMQKYLRTT KQQPYHTMES ILQHLEFCIT HDMTPKAFLE RYLAAGPTIQ YHKERWLAKQ WTLVSEEPVT NGLKD GIVF LLKRQDFSLV VSTKKVPFFK LSEEFVDPKS HKFVMRLQSE TSV

UniProtKB: Vang-like protein 2

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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

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116915
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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