[English] 日本語
Yorodumi
- EMDB-1965: Structural and Functional Studies of LRP6 Ectodomain Reveal a Pla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1965
TitleStructural and Functional Studies of LRP6 Ectodomain Reveal a Platform for Wnt Signaling
Map dataThis is a surface rendering of the ectodomain of LRP6 bound to its chaperone Mesd
Sample
  • Sample: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd
  • Protein or peptide: LDL-receptor-related protein 6
  • Protein or peptide: Mesoderm development protein
KeywordsLDL-receptor-related protein 6 / Wnt signaling pathway / Wnt co-receptor
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsChen S / Bubeck D / MacDonald BT / Liang WX / Mao JH / Malinauskas T / Llorca O / Aricescu AR / Siebold C / He X / Jones EY
CitationJournal: Dev Cell / Year: 2011
Title: Structural and functional studies of LRP6 ectodomain reveal a platform for Wnt signaling.
Authors: Shuo Chen / Doryen Bubeck / Bryan T MacDonald / Wen-Xue Liang / Jian-Hua Mao / Tomas Malinauskas / Oscar Llorca / A Radu Aricescu / Christian Siebold / Xi He / E Yvonne Jones /
Abstract: LDL-receptor-related protein 6 (LRP6), alongside Frizzled receptors, transduces Wnt signaling across the plasma membrane. The LRP6 ectodomain comprises four tandem β-propeller-EGF-like domain (PE) ...LDL-receptor-related protein 6 (LRP6), alongside Frizzled receptors, transduces Wnt signaling across the plasma membrane. The LRP6 ectodomain comprises four tandem β-propeller-EGF-like domain (PE) pairs that harbor binding sites for Wnt morphogens and their antagonists including Dickkopf 1 (Dkk1). To understand how these multiple interactions are integrated, we combined crystallographic analysis of the third and fourth PE pairs with electron microscopy (EM) to determine the complete ectodomain structure. An extensive inter-pair interface, conserved for the first-to-second and third-to-fourth PE interactions, contributes to a compact platform-like architecture, which is disrupted by mutations implicated in developmental diseases. EM reconstruction of the LRP6 platform bound to chaperone Mesd exemplifies a binding mode spanning PE pairs. Cellular and binding assays identify overlapping Wnt3a- and Dkk1-binding surfaces on the third PE pair, consistent with steric competition, but also suggest a model in which the platform structure supports an interplay of ligands through multiple interaction sites.
History
DepositionSep 12, 2011-
Header (metadata) releaseSep 30, 2011-
Map releaseOct 21, 2011-
UpdateOct 21, 2011-
Current statusOct 21, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0451
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0451
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1965_LRP6_ME...

Downloads & links

-
Map

FileDownload / File: emd_1965.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a surface rendering of the ectodomain of LRP6 bound to its chaperone Mesd
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.56 Å/pix.
x 60 pix.
= 273.6 Å		4.56 Å/pix.
x 60 pix.
= 273.6 Å		4.56 Å/pix.
x 60 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0451 / Movie #1: 0.0451
Minimum - Maximum-0.0474625 - 0.23142
Average (Standard dev.)0.00110932 (±0.0145592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 273.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.564.564.56
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z273.600273.600273.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-0.0470.2310.001

-
Supplemental data

-
Sample components

-
Entire : Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd

EntireName: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd
Components
  • Sample: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd
  • Protein or peptide: LDL-receptor-related protein 6
  • Protein or peptide: Mesoderm development protein

-
Supramolecule #1000: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd

SupramoleculeName: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd
type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: one LRP6 binds to one Mesd / Number unique components: 2
Molecular weightExperimental: 200 KDa / Method: Multi angle light scattering

-
Macromolecule #1: LDL-receptor-related protein 6

MacromoleculeName: LDL-receptor-related protein 6 / type: protein_or_peptide / ID: 1 / Name.synonym: LRP6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 100 KDa
Recombinant expressionOrganism: HEK293S / Recombinant plasmid: pHLsec vector

-
Macromolecule #2: Mesoderm development protein

MacromoleculeName: Mesoderm development protein / type: protein_or_peptide / ID: 2 / Name.synonym: Mesd / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 100 KDa
Recombinant expressionOrganism: HEK293S / Recombinant plasmid: pHLsec vector

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.015 mg/mL
BufferpH: 8 / Details: 150 mM NaCl,10 mM Tris-HCl
StainingType: NEGATIVE
Details: Grids were negatively stained with 0.75% uranyl formate using the two-drop method
GridDetails: carbon-coated copper grids
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 1230
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 4.56 µm / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal magnification: 72500
Sample stageSpecimen holder: single-tilt / Specimen holder model: JEOL

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, XMIPP / Number images used: 7928

+
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