[English] 日本語
Yorodumi
- EMDB-80088: receptor-arrestin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80088
Titlereceptor-arrestin
Map data
Sample
  • Complex: FZD6 beta-arrestin 1 complex
    • Protein or peptide: Isoform 1B of Beta-arrestin-1
    • Protein or peptide: heavy chain of scFv30
    • Protein or peptide: light chain of scFv30
    • Protein or peptide: Frizzled-6
KeywordsReceptor / Complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


midbrain morphogenesis / Signaling by RNF43 mutants / angiotensin receptor binding / Wnt receptor activity / non-canonical Wnt signaling pathway / TGFBR3 regulates TGF-beta signaling / Activation of SMO / Wnt-protein binding / apicolateral plasma membrane / negative regulation of interleukin-8 production ...midbrain morphogenesis / Signaling by RNF43 mutants / angiotensin receptor binding / Wnt receptor activity / non-canonical Wnt signaling pathway / TGFBR3 regulates TGF-beta signaling / Activation of SMO / Wnt-protein binding / apicolateral plasma membrane / negative regulation of interleukin-8 production / desensitization of G protein-coupled receptor signaling pathway / PCP/CE pathway / arrestin family protein binding / Class B/2 (Secretin family receptors) / G protein-coupled receptor internalization / stress fiber assembly / Wnt signaling pathway, planar cell polarity pathway / negative regulation of Notch signaling pathway / sensory perception / positive regulation of cardiac muscle hypertrophy / negative regulation of interleukin-6 production / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / canonical Wnt signaling pathway / pseudopodium / positive regulation of receptor internalization / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / clathrin-coated pit / intracellular glucose homeostasis / cytoplasmic vesicle membrane / Regulation of FZD by ubiquitination / enzyme inhibitor activity / negative regulation of canonical NF-kappaB signal transduction / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / negative regulation of canonical Wnt signaling pathway / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein phosphorylation / G protein-coupled receptor binding / G protein-coupled receptor activity / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / Ca2+ pathway / ubiquitin-dependent protein catabolic process / molecular adaptor activity / G alpha (s) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / transcription coactivator activity / apical plasma membrane / protein ubiquitination / Ub-specific processing proteases / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / chromatin / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Frizzled-6 / Frizzled 6, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain ...Frizzled-6 / Frizzled 6, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Immunoglobulin E-set
Similarity search - Domain/homology
Frizzled-6 / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFei X / Zhibin Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharmacol.Sin. / Year: 2026
Title: Direct beta-arrestin engagement by the non-canonical WNT receptor FZD6 via a shallow binding pocket
Authors: Zhang ZB / Lin X / Li MR / Pan YR / Kang Q / Xu F / Zhu XJ
History
DepositionApr 2, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_80088.png

Downloads & links

-
Map

FileDownload / File: emd_80088.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.)
0.54 Å/pix.
x 320 pix.
= 171.36 Å		0.54 Å/pix.
x 320 pix.
= 171.36 Å		0.54 Å/pix.
x 320 pix.
= 171.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5355 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0254
Minimum - Maximum-0.094165765 - 0.17547545
Average (Standard dev.)-0.00008271779 (±0.0072698737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin189191167
Dimensions320320320
Spacing320320320
CellA=B=C: 171.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_80088_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_80088_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FZD6 beta-arrestin 1 complex

EntireName: FZD6 beta-arrestin 1 complex
Components
  • Complex: FZD6 beta-arrestin 1 complex
    • Protein or peptide: Isoform 1B of Beta-arrestin-1
    • Protein or peptide: heavy chain of scFv30
    • Protein or peptide: light chain of scFv30
    • Protein or peptide: Frizzled-6

-
Supramolecule #1: FZD6 beta-arrestin 1 complex

SupramoleculeName: FZD6 beta-arrestin 1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Isoform 1B of Beta-arrestin-1

MacromoleculeName: Isoform 1B of Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.398629 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTVA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA LGVDYEVKAF VAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTVA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA LGVDYEVKAF VAENLEEKIH K RNSVRLVI RKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD IVLFNTA QYKVPVAMEE ADDTVAPSST FSKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRSSDVA VELPFTLMHP KPKEEPPHRE VPENETPVDT NLIELDTNDD DIVFEDFARQ RLKGMKDDKE EEED GTGSP QLNNR

UniProtKB: Beta-arrestin-1

-
Macromolecule #2: heavy chain of scFv30

MacromoleculeName: heavy chain of scFv30 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.294725 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MQVQLVESGG GLVQPGGSLR LSCAASGFNV YSSSIHWVRQ APGKGLEWVA SISSYYGYTY YADSVKGRFT ISADTSKNTA YLQMNSLRA EDTAVYYCAR SRQFWYSGLD YWGQGTLVTV SS

-
Macromolecule #3: light chain of scFv30

MacromoleculeName: light chain of scFv30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.717078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIK

-
Macromolecule #4: Frizzled-6

MacromoleculeName: Frizzled-6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.422824 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HSLFTCEPIT VPRCMKMAYN MTFFPNLMGH YDQSIAAVEM EHFLPLANLE CSPNIETFLC KAFVPTCIEQ IHVVPPCRKL CEKVYSDCK KLIDTFGIRW PEELECDRLQ YCDETVPVTF DPHTEFLGPQ KKTEQVQRDI GFWCPRHLKT SGGQGYKFLG I DQCAPPCP ...String:
HSLFTCEPIT VPRCMKMAYN MTFFPNLMGH YDQSIAAVEM EHFLPLANLE CSPNIETFLC KAFVPTCIEQ IHVVPPCRKL CEKVYSDCK KLIDTFGIRW PEELECDRLQ YCDETVPVTF DPHTEFLGPQ KKTEQVQRDI GFWCPRHLKT SGGQGYKFLG I DQCAPPCP NMYFKSDELE FAKSFIGTVS IFCLCATLFT FLTFLIDVRR FRYPERPIIY YSVCYSIVSL MYFIGFLLGD ST ACNKADE KLELGDTVVL GSQNKACTVL FMLLYFFTMA GTVWWVILTI TWFLAAGRKW SCEAIEQKAV WFHAVAWGTP GFL TVMLLA MNKVEGDNIS GVCFVGLYDL DASRYFVLLP LCLCVFVGLS LLLAGIISLN HVRQVIQHDG RNQEKLKKFM IRIG VFSGL YLVPLVTLLG CYVYEQVNRI TWEITWVSDH CRQYHIPCPY QAKAKARPEL ALFMIKYLMT LIVGISAVFW VGSKK TCTE WAGFFKRNRK RDPISESRRV LQEDE(SEP)C(TPO)(TPO)A (SEP)(SEP)(SEP)LAKDTSS

UniProtKB: Frizzled-6

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS 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: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8jh7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71056
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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