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- EMDB-1560: 3D structure of human chimeric endoglin-Fc -

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Basic information

Entry
Database: EMDB / ID: EMD-1560
Title3D structure of human chimeric endoglin-Fc
Map dataThis is a chimeric protein of the extracellular region of endoglin fused to the Fc fragment of the human IgG1
Sample
  • Sample: Extracellular region of human endoglin (Glu26-Gly586), tagged with an HA epitope in N-ter and a Fc fragment in C-ter.
  • Protein or peptide: Chimeric receptor
KeywordsEndoglin / CD105 / TGF-beta / HHT disorder / zona pellucida / preeclampsia / fusion protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 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 26, 2008-
Header (metadata) releaseSep 29, 2008-
Map releaseApr 2, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1560.gif

Downloads & links

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Map

FileDownload / File: emd_1560.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a chimeric protein of the extracellular region of endoglin fused to the Fc fragment of the human IgG1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 80 pix.
= 184. Å		2.3 Å/pix.
x 80 pix.
= 184. Å		2.3 Å/pix.
x 80 pix.
= 184. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.28 / Movie #1: 3.3
Minimum - Maximum-4.06402 - 9.12504
Average (Standard dev.)0.128689 (±0.769056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 184 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z184.000184.000184.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-4.0649.1250.129

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Supplemental data

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Sample components

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Entire : Extracellular region of human endoglin (Glu26-Gly586), tagged wit...

EntireName: Extracellular region of human endoglin (Glu26-Gly586), tagged with an HA epitope in N-ter and a Fc fragment in C-ter.
Components
  • Sample: Extracellular region of human endoglin (Glu26-Gly586), tagged with an HA epitope in N-ter and a Fc fragment in C-ter.
  • Protein or peptide: Chimeric receptor

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Supramolecule #1000: Extracellular region of human endoglin (Glu26-Gly586), tagged wit...

SupramoleculeName: Extracellular region of human endoglin (Glu26-Gly586), tagged with an HA epitope in N-ter and a Fc fragment in C-ter.
type: sample / ID: 1000 / Oligomeric state: One homodimer / Number unique components: 1
Molecular weightExperimental: 210 KDa / Theoretical: 190 KDa / Method: SDS-PAGE

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Macromolecule #1: Chimeric receptor

MacromoleculeName: Chimeric receptor / type: protein_or_peptide / ID: 1 / Name.synonym: EndoEC-Fc / Number of copies: 2 / Oligomeric state: Homodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Culture supernatant
Molecular weightExperimental: 210 KDa / Theoretical: 190 KDa
Recombinant expressionOrganism: CHO-K1 / Recombinant plasmid: pDisplay

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7 / Details: 150mM NaCl, 50mM Na2HPO4, 10% glycerol
StainingType: NEGATIVE
Details: EndoEC-Fc 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

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Electron microscopy

MicroscopeJEOL 1230
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
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5741
Final two d classificationNumber classes: 153

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