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- EMDB-1213: Structural model for the mannose receptor family uncovered by ele... -

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Basic information

Entry
Database: EMDB / ID: EMD-1213
TitleStructural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor.
Map dataThis a 3D reconstruction of the soluble fragment of the mannose receptor
Sample
  • Sample: Soluble Form of Mouse Mannose Receptor
  • Protein or peptide: Mannose Receptor
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 33.0 Å
AuthorsBoskovic J / Arnold JN / Stilion R / Gordon S / Sim RB / Rivera-Calzada A / Wienke D / Isacke CM / Martinez-Pomares L / Llorca O
CitationJournal: J Biol Chem / Year: 2006
Title: Structural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor.
Authors: Jasminka Boskovic / James N Arnold / Richard Stilion / Siamon Gordon / Robert B Sim / Angel Rivera-Calzada / Dirk Wienke / Clare M Isacke / Luisa Martinez-Pomares / Oscar Llorca /
Abstract: The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A(2) receptor (PLA(2)R) and the mannose receptor (MR, CD206), whose extracellular ...The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A(2) receptor (PLA(2)R) and the mannose receptor (MR, CD206), whose extracellular portion contains a similar domain arrangement: an N-terminal cysteine-rich domain (CysR) followed by a single fibronectin type II domain (FNII) and 8-10 C-type lectin-like domains (CTLDs). These proteins mediate diverse functions ranging from extracellular matrix turnover through collagen uptake to homeostasis and immunity based on sugar recognition. Endo180 and the MR are multivalent transmembrane receptors capable of interacting with multiple ligands; in both receptors FNII recognizes collagens, and a single CTLD retains lectin activity (CTLD2 in Endo180 and CTLD4 in MR). It is expected that the overall conformation of these multivalent molecules would deeply influence their function as the availability of their binding sites could be altered under different conditions. However, conflicting reports have been published on the three-dimensional arrangement of these receptors. Here, we have used single particle electron microscopy to elucidate the three-dimensional organization of the MR and Endo180. Strikingly, we have found that both receptors display distinct three-dimensional structures, which are, however, conceptually very similar: a bent and compact conformation built upon interactions of the CysR domain and the lone functional CTLD. Biochemical and electron microscopy experiments indicate that, under a low pH mimicking the endosomal environment, both MR and Endo180 experience large conformational changes. We propose a structural model for the mannose receptor family where at least two conformations exist that may serve to regulate differences in ligand selectivity.
History
DepositionFeb 9, 2006-
Header (metadata) releaseApr 3, 2006-
Map releaseApr 3, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.489813226
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.489813226
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1213.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis a 3D reconstruction of the soluble fragment of the mannose receptor
Voxel sizeX=Y=Z: 5.3 Å
Density
Contour Level1: 1.88 / Movie #1: 3.4898132
Minimum - Maximum-3.7008 - 9.32741
Average (Standard dev.)0.00000000175807 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-24-24-24
Dimensions484848
Spacing484848
CellA=B=C: 254.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.35.35.3
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-3.7019.3270.000

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Supplemental data

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Sample components

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Entire : Soluble Form of Mouse Mannose Receptor

EntireName: Soluble Form of Mouse Mannose Receptor
Components
  • Sample: Soluble Form of Mouse Mannose Receptor
  • Protein or peptide: Mannose Receptor

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Supramolecule #1000: Soluble Form of Mouse Mannose Receptor

SupramoleculeName: Soluble Form of Mouse Mannose Receptor / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightExperimental: 160 KDa / Theoretical: 180 KDa / Method: Gel Filtration Chromatography

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Macromolecule #1: Mannose Receptor

MacromoleculeName: Mannose Receptor / type: protein_or_peptide / ID: 1 / Name.synonym: MR
Details: MR(CD206) is a member of mannose receptor family of transmembrane receptors which acts as a molecular scavenger that binds and internalises potentially harmful glycoproteins and may also ...Details: MR(CD206) is a member of mannose receptor family of transmembrane receptors which acts as a molecular scavenger that binds and internalises potentially harmful glycoproteins and may also mediate phagocytosis of a wide variety of microbes.
Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse / Organelle: Supernatant / Location in cell: membrane
Molecular weightExperimental: 180 KDa / Theoretical: 160 KDa
Recombinant expressionOrganism: 293T / Recombinant plasmid: pMH

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: 10mMTris,140mM Nacl,10 mM CaCl2
StainingType: NEGATIVE
Details: Protein was adsorbed to glow-discharged carbon-coated grids and negatively stained with 2% w/v uranyl acetate
GridDetails: 400 mesh copper-rhodium grid
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeJEOL 1230
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.9 mm / Nominal magnification: 40000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DetailsElectron microscope was JEOL JEM-120, 120kV. Specimen holder, JEOL type M: 207EM-11020. Images were colected in low-dose conditions
Image recordingCategory: FILM / Film or detector model: KODAK 4489 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 5.3 µm / Details: Minolta Dimage Scan Multi Pro. Scan at 2400 dpi / Bits/pixel: 16

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Angular refinement using a blob as starting reference volume
Number images used: 7322
DetailsParticles were selected using boxer program from EMAN (J.Struct.Biol. (1999) 128:82-97)

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Atomic model buiding 1

Initial model(PDB ID:
,
,
,
)
DetailsProtocol: Rigid Body. Fiting was performed manually using UCSF Chimera package (J. Comput. Chem. (2004: 24, 1605-1612)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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