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- PDB-9jk6: Human VANGL1 hexamer -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9jk6
TitleHuman VANGL1 hexamer
ComponentsVang-like protein 1
KeywordsMEMBRANE PROTEIN / VANGL / Planar cell polarity / PCP
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsSong, Y. / Zhang, Z. / Jian, S. / Zheng, P.
Funding support China, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vang-like protein 1
B: Vang-like protein 1
C: Vang-like protein 1
D: Vang-like protein 1
E: Vang-like protein 1
F: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)363,7476
Polymers363,7476
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Vang-like protein 1 / Loop-tail protein 2 homolog / LPP2 / Strabismus 2 / Van Gogh-like protein 1


Mass: 60624.523 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VANGL1, STB2 / Production host: Homo sapiens (human) / References: UniProt: Q8TAA9
Has protein modificationY

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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: VANGL1 hexamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54018 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00518924
ELECTRON MICROSCOPYf_angle_d0.86725602
ELECTRON MICROSCOPYf_dihedral_angle_d19.3946978
ELECTRON MICROSCOPYf_chiral_restr0.052922
ELECTRON MICROSCOPYf_plane_restr0.0073186

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