[English] 日本語
Yorodumi
- EMDB-61547: Human VANGL1 in complex with PK1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61547
TitleHuman VANGL1 in complex with PK1
Map data
Sample
  • Complex: VANGL1-PK1 complex
    • Protein or peptide: Vang-like protein 1
KeywordsVANGL / Planar cell polarity / PCP / Prickle1 / MEMBRANE 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 / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / lateral plasma membrane / 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: 2.6 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

-
Structure visualization

Supplemental images

emd_61547.png

Downloads & links

-
Map

FileDownload / File: emd_61547.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6612388 - 1.0326107
Average (Standard dev.)0.0004030291 (±0.019343166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_61547_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61547_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61547_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : VANGL1-PK1 complex

EntireName: VANGL1-PK1 complex
Components
  • Complex: VANGL1-PK1 complex
    • Protein or peptide: Vang-like protein 1

-
Supramolecule #1: VANGL1-PK1 complex

SupramoleculeName: VANGL1-PK1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

-
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: 60.624523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPSRATMDTE STYSGYSYYS SHSKKSHRQG ERTRERHKSP RNKDGRGSEK SVTIQPPTGE PLLGNDSTRT EEVQDDNWGE TTTAITGTS EHSISQEDIA RISKDMEDSV GLDCKRYLGL TVASFLGLLV FLTPIAFILL PPILWRDELE PCGTICEGLF I SMAFKLLI ...String:
GPSRATMDTE STYSGYSYYS SHSKKSHRQG ERTRERHKSP RNKDGRGSEK SVTIQPPTGE PLLGNDSTRT EEVQDDNWGE TTTAITGTS EHSISQEDIA RISKDMEDSV GLDCKRYLGL TVASFLGLLV FLTPIAFILL PPILWRDELE PCGTICEGLF I SMAFKLLI LLIGTWALFF RKRRADMPRV FVFRALLLVL IFLFVVSYWL FYGVRILDSR DRNYQGIVQY AVSLVDALLF IH YLAIVLL ELRQLQPMFT LQVVRSTDGE SRFYSLGHLS IQRAALVVLE NYYKDFTIYN PNLLTASKFR AAKHMAGLKV YNV DGPSNN ATGQSRAMIA AAARRRDSSH NELYYEEAEH ERRVKKRKAR LVVAVEEAFI HIQRLQAEEQ QKAPGEVMDP REAA QAIFP SMARALQKYL RITRQQNYHS MESILQHLAF CITNGMTPKA FLERYLSAGP TLQYDKDRWL STQWRLVSDE AVTNG LRDG IVFVLKCLDF SLVVNVKKIP FIILSEEFID PKSHKFVLRL QSETSV

UniProtKB: Vang-like protein 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60117
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more