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- EMDB-1977: Extracellular complexes of the hematopoietic human and mouse CSF-... -

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Basic information

Entry
Database: EMDB / ID: EMD-1977
TitleExtracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles.
Map dataSurface rendering of the hCSF-1RD1-D5 hCSF-1 complex
Sample
  • Sample: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R
  • Protein or peptide: Colony Stimulating Factor-1 Receptor (CSF-1R)
  • Protein or peptide: Colony Stimulating Factor-1
KeywordsHematopoiesis / Receptor Tyrosine Kinase (RTK) / Colony-Stimulating Factor-1 / CSF-1 / CSF-1R / ternary complex / ectodomain complex / cytokine-receptor complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsElegheert J / Desfosses A / Shkumatov AV / Wu X / Bracke N / Verstraete K / Van Craenenbroeck K / Brooks BR / Svergun DI / Vergauwen B ...Elegheert J / Desfosses A / Shkumatov AV / Wu X / Bracke N / Verstraete K / Van Craenenbroeck K / Brooks BR / Svergun DI / Vergauwen B / Gutsche I / Savvides SN
CitationJournal: Structure / Year: 2011
Title: Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles.
Authors: Jonathan Elegheert / Ambroise Desfosses / Alexander V Shkumatov / Xiongwu Wu / Nathalie Bracke / Kenneth Verstraete / Kathleen Van Craenenbroeck / Bernard R Brooks / Dmitri I Svergun / Bjorn ...Authors: Jonathan Elegheert / Ambroise Desfosses / Alexander V Shkumatov / Xiongwu Wu / Nathalie Bracke / Kenneth Verstraete / Kathleen Van Craenenbroeck / Bernard R Brooks / Dmitri I Svergun / Bjorn Vergauwen / Irina Gutsche / Savvas N Savvides /
Abstract: The hematopoietic colony stimulating factor-1 receptor (CSF-1R or FMS) is essential for the cellular repertoire of the mammalian immune system. Here, we report a structural and mechanistic consensus ...The hematopoietic colony stimulating factor-1 receptor (CSF-1R or FMS) is essential for the cellular repertoire of the mammalian immune system. Here, we report a structural and mechanistic consensus for the assembly of human and mouse CSF-1:CSF-1R complexes. The EM structure of the complete extracellular assembly of the human CSF-1:CSF-1R complex reveals how receptor dimerization by CSF-1 invokes a ternary complex featuring extensive homotypic receptor contacts and striking structural plasticity at the extremities of the complex. Studies by small-angle X-ray scattering of unliganded hCSF-1R point to large domain rearrangements upon CSF-1 binding, and provide structural evidence for the relevance of receptor predimerization at the cell surface. Comparative structural and binding studies aiming to dissect the assembly principles of human and mouse CSF-1R complexes, including a quantification of the CSF-1/CSF-1R species cross-reactivity, show that bivalent cytokine binding to receptor coupled to ensuing receptor-receptor interactions are common denominators in extracellular complex formation.
History
DepositionOct 17, 2011-
Header (metadata) releaseOct 21, 2011-
Map releaseDec 16, 2011-
UpdateMay 3, 2012-
Current statusMay 3, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1977_CSF1R_i...

Downloads & links

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Map

FileDownload / File: emd_1977.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendering of the hCSF-1RD1-D5 hCSF-1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 80 pix.
= 280. Å		3.5 Å/pix.
x 80 pix.
= 280. Å		3.5 Å/pix.
x 80 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.01 / Movie #1: 0.015
Minimum - Maximum-0.03322909 - 0.22371151
Average (Standard dev.)-0.0002531 (±0.00919499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
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/NS808080
D min/max/mean-0.0330.224-0.000

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Supplemental data

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Sample components

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Entire : Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the co...

EntireName: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R
Components
  • Sample: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R
  • Protein or peptide: Colony Stimulating Factor-1 Receptor (CSF-1R)
  • Protein or peptide: Colony Stimulating Factor-1

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Supramolecule #1000: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the co...

SupramoleculeName: Complex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R
type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Dimeric / Number unique components: 2
Molecular weightExperimental: 145 KDa / Theoretical: 145 KDa / Method: Multi-angle laser light scattering

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Macromolecule #1: Colony Stimulating Factor-1 Receptor (CSF-1R)

MacromoleculeName: Colony Stimulating Factor-1 Receptor (CSF-1R) / type: protein_or_peptide / ID: 1 / Name.synonym: CSF-1R / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 76 KDa / Theoretical: 76 KDa
Recombinant expressionOrganism: Homo sapiens, HEK293T cell line / Recombinant plasmid: pHLSec

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Macromolecule #2: Colony Stimulating Factor-1

MacromoleculeName: Colony Stimulating Factor-1 / type: protein_or_peptide / ID: 2 / Name.synonym: CSF-1 / Number of copies: 2 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Homo sapiens, HEK293T cell line / Recombinant plasmid: pHLSec

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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

BufferpH: 7.5 / Details: 20 mM NaPO4 pH 7.40, 150 mM NaCl.
StainingType: NEGATIVE
Details: Purified sample at 0.2 mg/mL in PBS buffer was applied to the clear side of carbon on a carbon-mica interface and stained by floating on 2 % (w/v) uranyl acetate.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1200EXII
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Bits/pixel: 8
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.1 mm / Nominal magnification: 40000
Sample stageSpecimen holder: Jeol / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: CTFFIND3. Each particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER / Number images used: 9421

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