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

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Entry
Database: EMDB / ID: 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
SampleComplex of human Colony-Stimulating Factor-1 (hCSF-1) with the complete ectodomain of hCSF-1R:
(Colony Stimulating Factor- ...) x 2
KeywordsHematopoiesis / Receptor Tyrosine Kinase (RTK) / Colony-Stimulating Factor-1 / CSF-1 / CSF-1R / ternary complex / ectodomain complex / cytokine-receptor complex
SourceHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / 23 Å resolution
AuthorsElegheert 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 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.
DateDeposition: Oct 17, 2011 / Header (metadata) release: Oct 21, 2011 / Map release: Dec 16, 2011 / Last update: May 3, 2012

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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
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Structure viewerEM map:
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Supplemental images

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Map

Fileemd_1977.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

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Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
3.5 Å/pix.
= 280. Å
80 pix
3.5 Å/pix.
= 280. Å
80 pix
3.5 Å/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
Contour Level:0.01 (by emdb), 0.015 (movie #1):
Minimum - Maximum-0.03322909 - 0.22371151
Average (Standard dev.)-0.00025310 (0.00919499)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
CellA=B=C: 280.0 Å
α=β=γ: 90.0 deg.

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
Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: Dimeric
MassTheoretical: 145 kDa / Experimental: 145 kDa / Measured by: Multi-angle laser light scattering

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Component #1: protein, Colony Stimulating Factor-1 Receptor (CSF-1R)

ProteinName: Colony Stimulating Factor-1 Receptor (CSF-1R) / a.k.a: CSF-1R / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 76 kDa / Experimental: 76 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens, HEK293T cell line / Vector: pHLSec

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Component #2: protein, Colony Stimulating Factor-1

ProteinName: Colony Stimulating Factor-1 / a.k.a: CSF-1 / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 2
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens, HEK293T cell line / Vector: pHLSec

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionBuffer solution: 20 mM NaPO4 pH 7.40, 150 mM NaCl. / pH: 7.5
StainingPurified 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.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 1200EXII
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: OTHER
LensMagnification: 40000 X (nominal) / Cs: 2.1 mm / Imaging mode: OTHER
Specimen HolderHolder: Jeol / Model: JEOL
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 9421 / Applied symmetry: C2 (2 fold cyclic)
3D reconstructionAlgorithm: Angular Reconstitution and Projection matching / Software: IMAGIC, SPIDER / CTF correction: CTFFIND3. Each particle / Resolution: 23 Å / Resolution method: FSC 0.5

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