4WRL

Structure of the human CSF-1:CSF-1R complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure and Assembly Mechanism of the Signaling Complex Mediated by Human CSF-1.

Felix, J.De Munck, S.Verstraete, K.Meuris, L.Callewaert, N.Elegheert, J.Savvides, S.N.

(2015) Structure 23: 1621-1631

  • DOI: 10.1016/j.str.2015.06.019
  • Primary Citation of Related Structures:  
    4WRL, 4WRM

  • PubMed Abstract: 
  • Human colony-stimulating factor 1 receptor (hCSF-1R) is unique among the hematopoietic receptors because it is activated by two distinct cytokines, CSF-1 and interleukin-34 (IL-34). Despite ever-growing insights into the central role of hCSF-1R signaling in innate and adaptive immunity, inflammatory diseases, and cancer, the structural basis of the functional dichotomy of hCSF-1R has remained elusive ...

    Human colony-stimulating factor 1 receptor (hCSF-1R) is unique among the hematopoietic receptors because it is activated by two distinct cytokines, CSF-1 and interleukin-34 (IL-34). Despite ever-growing insights into the central role of hCSF-1R signaling in innate and adaptive immunity, inflammatory diseases, and cancer, the structural basis of the functional dichotomy of hCSF-1R has remained elusive. Here, we report crystal structures of ternary complexes between hCSF-1 and hCSF-1R, including their complete extracellular assembly, and propose a mechanism for the cooperative human CSF-1:CSF-1R complex that relies on the adoption by dimeric hCSF-1 of an active conformational state and homotypic receptor interactions. Furthermore, we trace the cytokine-binding duality of hCSF-1R to a limited set of conserved interactions mediated by functionally equivalent residues on CSF-1 and IL-34 that play into the geometric requirements of hCSF-1R activation, and map the possible mechanistic consequences of somatic mutations in hCSF-1R associated with cancer.


    Organizational Affiliation

    Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium; Unit for Structural Biology, VIB Inflammation Research Center, 9052 Ghent, Belgium. Electronic address: savvas.savvides@ugent.be.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor AC286Homo sapiensMutation(s): 1 
Gene Names: CSF1RFMS
EC: 2.7.10.1
Find proteins for P07333 (Homo sapiens)
Explore P07333 
Go to UniProtKB:  P07333
NIH Common Fund Data Resources
PHAROS:  P07333
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 BD170Homo sapiensMutation(s): 0 
Gene Names: CSF1
Find proteins for P09603 (Homo sapiens)
Explore P09603 
Go to UniProtKB:  P09603
NIH Common Fund Data Resources
PHAROS:  P09603
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, H
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, I
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA

Download Ideal Coordinates CCD File 
A
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900067
Query on PRD_900067
G, I3'-sialyl-N-acetyllactosamineOligosaccharide /  Substrate analog

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.997α = 90
b = 142.997β = 90
c = 138.323γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary