[English] 日本語
Yorodumi
- EMDB-19881: High resolution structure of FZD7 in inactive conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19881
TitleHigh resolution structure of FZD7 in inactive conformation
Map dataHigh resolution structure of inactive FZD7
Sample
  • Complex: FZD7 anti-parallel Dimer
    • Protein or peptide: Frizzled-7
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: PALMITIC ACID
  • Ligand: water
KeywordsGPCPR / Frizzled / FZD7 / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / somatic stem cell division / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / somatic stem cell division / Wnt receptor activity / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / regulation of canonical Wnt signaling pathway / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / canonical Wnt signaling pathway / positive regulation of phosphorylation / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / PDZ domain binding / G protein-coupled receptor activity / positive regulation of JNK cascade / neuron differentiation / recycling endosome membrane / T cell differentiation in thymus / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / membrane / plasma membrane
Similarity search - Function
Frizzled-7, cysteine-rich Wnt-binding 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. ...Frizzled-7, cysteine-rich Wnt-binding 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. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Biological speciesSpodoptera frugiperda (fall armyworm) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsBous J / Kinsolving J / Gratz L / Scharf MM / Voss J / Selcuk B / Adebali O / Schulte G
Funding support Sweden, Germany, 7 items
OrganizationGrant numberCountry
Other government2021-00430 (Karolinska Instutet) Sweden
Swedish Research Council2019-01190 Sweden
Other government20 1102 (Swedish Cancer Society) Sweden
Other government23 2825 (Swedish Cancer Society) Sweden
Other privateUPD2021-0029 (Wenner Gren Foundation) Sweden
German Research Foundation (DFG)504098926 Germany
German Research Foundation (DFG)520506488 Germany
CitationJournal: To Be Published
Title: high-resolution structural characterization of FZD7 unravels the importance of water network and cholesterol for class F GPCRs dynamic and activation
Authors: Bous J / Kinsolving J / Gratz L / Scharf MM / Voss J / Selcuk B / Adebali O / Schulte G
History
DepositionMar 19, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19881.png

Downloads & links

-
Map

FileDownload / File: emd_19881.map.gz / Format: CCP4 / Size: 199.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHigh resolution structure of inactive FZD7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 374 pix.
= 253.123 Å		0.68 Å/pix.
x 374 pix.
= 253.123 Å		0.68 Å/pix.
x 374 pix.
= 253.123 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6768 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.31717828 - 0.62563175
Average (Standard dev.)-0.00017869218 (±0.010248303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions374374374
Spacing374374374
CellA=B=C: 253.1232 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19881_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: High resolution structure of inactive FZD7 (halph map 1)

Fileemd_19881_half_map_1.map
AnnotationHigh resolution structure of inactive FZD7 (halph map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: High resolution structure of inactive FZD7 (half map 2)

Fileemd_19881_half_map_2.map
AnnotationHigh resolution structure of inactive FZD7 (half map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FZD7 anti-parallel Dimer

EntireName: FZD7 anti-parallel Dimer
Components
  • Complex: FZD7 anti-parallel Dimer
    • Protein or peptide: Frizzled-7
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: PALMITIC ACID
  • Ligand: water

-
Supramolecule #1: FZD7 anti-parallel Dimer

SupramoleculeName: FZD7 anti-parallel Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 134788 kDa/nm

-
Macromolecule #1: Frizzled-7

MacromoleculeName: Frizzled-7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.460859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDQPYHGEK GISVPDHGFC QPISIPLCTD IAYNQTILPN LLGHTNQEDA GLEVHQFYPL VKVQCSPEL RFFLCSMYAP VCTVLDQAIP PCRSLCERAR QGCEALMNKF GFQWPERLRC ENFPVHGAGE ICVGQNTSDG S GGPGGGPT ...String:
MKTIIALSYI FCLVFADYKD DDDQPYHGEK GISVPDHGFC QPISIPLCTD IAYNQTILPN LLGHTNQEDA GLEVHQFYPL VKVQCSPEL RFFLCSMYAP VCTVLDQAIP PCRSLCERAR QGCEALMNKF GFQWPERLRC ENFPVHGAGE ICVGQNTSDG S GGPGGGPT AYPTAPYLPD LPFTALPPGA SDGRGRPAFP FSCPRQLKVP PYLGYRFLGE RDCGAPCEPG RANGLMYFKE EE RRFARLW VGVWSVLCCA STLFTVLTYL VDMRRFSYPE RPIIFLSGCY FMVAVAHVAG FLLEDRAVCV ERFSDDGYRT VAQ GTKKEG CTILFMVLYF FGMASSIWWV ILSLTWFLAA GMKWGHEAIE ANSQYFHLAA WAVPAVKTIT ILAMGQVDGD LLSG VCYVG LSSVDALRGF VLAPLFVYLF IGTSFLLAGF VSLFRIRTIM KHDGTKTEKL EKLMVRIGVF SVLYTVPATI VLACY FYEQ AFREHWERTW LLQTCKSYAV PCPPGHFPPM SPDFTVFMIK YLMTMIVGIT TGFWIWSGKT LQSWRRFYHR LSHSSK GET AVSRLEVLFQ GPWSHPQFEK GGGSGGGSGG GSWSHPQFEK

UniProtKB: Frizzled-7

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 94 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.08 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.01 MTRIS-HCLtris hydrochloride
0.1 MNaClSodium Chloride
0.0002 %CHScholesteryl hemisuccinate tris salt
0.002 %LMNGLauryl Maltose Neopentyl Glycol
0.0002 %GDNglyco-diosgenin
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 21081 / Average exposure time: 3.5 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 7332734
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7evw
PDB Unreleased entry


Details: chain R
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 145595
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7evw
PDB Unreleased entry


Chain - Chain ID: R / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9epo:
High resolution structure of FZD7 in inactive conformation

+
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