[English] 日本語
Yorodumi
- EMDB-1559: 3D structure of human endoglin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1559
Title3D structure of human endoglin
Map datastructure of human endoglin
Sample
  • Sample: Extracellular region of human endoglin, from Glu26 to Leu587 residues.
  • Protein or peptide: Transmembrane receptorCell surface receptor
KeywordsEndoglin / CD105 / TGF-beta / HHT disorder / zona pellucida / preeclampsia
Function / homologyZona pellucida domain / regulation of transforming growth factor beta receptor signaling pathway
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLlorca O / Trujillo A / Blanco FJ / Bernabeu C
CitationJournal: J Mol Biol / Year: 2007
Title: Structural model of human endoglin, a transmembrane receptor responsible for hereditary hemorrhagic telangiectasia.
Authors: Oscar Llorca / Arturo Trujillo / Francisco J Blanco / Carmelo Bernabeu /
Abstract: Endoglin is a type I membrane protein expressed as a disulphide-linked homodimer on human vascular endothelial cells whose haploinsufficiency is responsible for the dominant vascular dysplasia known ...Endoglin is a type I membrane protein expressed as a disulphide-linked homodimer on human vascular endothelial cells whose haploinsufficiency is responsible for the dominant vascular dysplasia known as hereditary hemorrhagic telangiectasia (HHT). Structurally, endoglin belongs to the zona pellucida (ZP) family of proteins that share a ZP domain of approximately 260 amino acid residues at their extracellular region. Endoglin is a component of the TGF-beta receptor complex, interacts with the TGF-beta signalling receptors types I and II, and modulates cellular responses to TGF-beta. Here, we have determined for the first time the three-dimensional structure of the approximately 140 kDa extracellular domain of endoglin at 25 A resolution, using single-particle electron microscopy (EM). This reconstruction provides the general architecture of endoglin, which arranges as a dome made of antiparallel oriented monomers enclosing a cavity at one end. A high-resolution structure of endoglin has also been modelled de novo and found to be consistent with the experimental reconstruction. Each subunit comprises three well-defined domains, two of them corresponding to ZP regions, organised into an open U-shaped monomer. This domain arrangement was found to closely resemble the overall structure derived experimentally and the three modelled de novo domains were tentatively assigned to the domains observed in the EM reconstruction. This molecular model was further tested by tagging endoglin's C terminus with an IgG Fc fragment visible after 3D reconstruction of the labelled protein. Combined, these data provide the structural framework to interpret endoglin's functional domains and mutations found in HHT patients.
History
DepositionSep 25, 2008-
Header (metadata) releaseSep 26, 2008-
Map releaseApr 2, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.651733
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.651733
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1559.gif

Downloads & links

-
Map

FileDownload / File: emd_1559.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of human endoglin
Voxel sizeX=Y=Z: 2.3 Å
Density
Contour LevelBy AUTHOR: 2.17 / Movie #1: 3.651733
Minimum - Maximum-3.66604 - 7.95689
Average (Standard dev.)0.0000000130307 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin186186186
Dimensions808080
Spacing808080
CellA=B=C: 368 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z368.000368.000368.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS186186186
NC/NR/NS808080
D min/max/mean-3.6667.9570.000

-
Supplemental data

-
Sample components

-
Entire : Extracellular region of human endoglin, from Glu26 to Leu587 residues.

EntireName: Extracellular region of human endoglin, from Glu26 to Leu587 residues.
Components
  • Sample: Extracellular region of human endoglin, from Glu26 to Leu587 residues.
  • Protein or peptide: Transmembrane receptorCell surface receptor

-
Supramolecule #1000: Extracellular region of human endoglin, from Glu26 to Leu587 residues.

SupramoleculeName: Extracellular region of human endoglin, from Glu26 to Leu587 residues.
type: sample / ID: 1000 / Oligomeric state: One disulphide-linked homodimer / Number unique components: 1
Molecular weightExperimental: 130 KDa / Theoretical: 140 KDa / Method: SDS-PAGE

-
Macromolecule #1: Transmembrane receptor

MacromoleculeName: Transmembrane receptor / type: protein_or_peptide / ID: 1 / Name.synonym: Endoglin / Number of copies: 2 / Oligomeric state: Homodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightExperimental: 130 KDa / Theoretical: 140 KDa
Recombinant expressionOrganism: Mouse myeloma cell line NS0
SequenceGO: regulation of transforming growth factor beta receptor signaling pathway
InterPro: Zona pellucida domain

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7 / Details: 150mM NaCl, 50mM Na2HPO4, 10% glycerol
StainingType: NEGATIVE
Details: EndoEC was applied to carbon-coated grids and negatively stained with 1% w/v uranyl acetate.
GridDetails: 40 mesh Copper/Palladium grid.
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 1230
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.9 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Alignment procedureLegacy - Astigmatism: Correction with FFT and CCD camera
DetailsMicroscope used JEOL-1230
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm
Details: Images scanned with a MINOLTA Dimage Scan Multi Pro scanner at 2400 dpi
Bits/pixel: 16

-
Image processing

Final two d classificationNumber classes: 16
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 2964

+
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