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- PDB-3uf2: Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-... -

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Basic information

Entry
Database: PDB / ID: 3uf2
TitleCrystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine
ComponentsMacrophage colony-stimulating factor 1
KeywordsCYTOKINE / hematopoietic cytokine / RTKIII / Four-helix bundle
Function / homology
Function and homology information


regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / positive regulation of macrophage migration / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction ...regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / positive regulation of macrophage migration / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / CSF1-CSF1R complex / monocyte activation / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / mammary duct terminal end bud growth / microglial cell proliferation / positive regulation of mononuclear cell proliferation / positive regulation of macrophage differentiation / myeloid leukocyte migration / neutrophil homeostasis / positive regulation of monocyte differentiation / positive regulation of multicellular organism growth / positive regulation of osteoclast differentiation / branching involved in mammary gland duct morphogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of Ras protein signal transduction / Other interleukin signaling / positive regulation of cell-matrix adhesion / positive regulation of macrophage chemotaxis / Interleukin-10 signaling / positive regulation of protein metabolic process / macrophage differentiation / monocyte differentiation / regulation of ossification / Transcriptional and post-translational regulation of MITF-M expression and activity / homeostasis of number of cells within a tissue / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / response to ischemia / cytokine activity / Post-translational protein phosphorylation / growth factor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by CSF1 (M-CSF) in myeloid cells / Ras protein signal transduction / nuclear body / positive regulation of cell migration / endoplasmic reticulum lumen / inflammatory response / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsElegheert, J. / Savvides, S.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1
Authors: Elegheert, J. / Bracke, N. / Pouliot, P. / Gutsche, I. / Shkumatov, A.V. / Tarbouriech, N. / Verstraete, K. / Bekaert, A. / Burmeister, W.P. / Svergun, D.I. / Lambrecht, B.N. / Vergauwen, B. / Savvides, S.N.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage colony-stimulating factor 1
B: Macrophage colony-stimulating factor 1
C: Macrophage colony-stimulating factor 1
D: Macrophage colony-stimulating factor 1
E: Macrophage colony-stimulating factor 1
F: Macrophage colony-stimulating factor 1
G: Macrophage colony-stimulating factor 1
H: Macrophage colony-stimulating factor 1
I: Macrophage colony-stimulating factor 1
J: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)178,68210
Polymers178,68210
Non-polymers00
Water3,045169
1
A: Macrophage colony-stimulating factor 1
B: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)35,7362
Polymers35,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area14310 Å2
MethodPISA
2
C: Macrophage colony-stimulating factor 1
D: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)35,7362
Polymers35,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-11 kcal/mol
Surface area14370 Å2
MethodPISA
3
E: Macrophage colony-stimulating factor 1
F: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)35,7362
Polymers35,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area14490 Å2
MethodPISA
4
G: Macrophage colony-stimulating factor 1
H: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)35,7362
Polymers35,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-14 kcal/mol
Surface area14450 Å2
MethodPISA
5
I: Macrophage colony-stimulating factor 1
J: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)35,7362
Polymers35,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 104.490, 116.240
Angle α, β, γ (deg.)90.00, 105.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Macrophage colony-stimulating factor 1 / CSF-1 / M-CSF / MCSF / Lanimostim / Processed macrophage colony-stimulating factor 1


Mass: 17868.219 Da / Num. of mol.: 10 / Fragment: UNP RESIDUES 33-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: P09603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2009
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. all: 36596 / Num. obs: 36596 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.75→3 Å / % possible all: 98.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_874) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→24.942 Å / σ(F): 2 / Phase error: 30.17 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 3663 10.02 %random
Rwork0.1373 ---
all0.1423 36555 --
obs0.1423 36555 99.62 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.94 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.3668 Å2-0 Å21.9836 Å2
2---15.4315 Å2-0 Å2
3----17.9221 Å2
Refinement stepCycle: LAST / Resolution: 2.75→24.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11351 0 0 169 11520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211662
X-RAY DIFFRACTIONf_angle_d0.48715665
X-RAY DIFFRACTIONf_dihedral_angle_d14.1834413
X-RAY DIFFRACTIONf_chiral_restr0.0341775
X-RAY DIFFRACTIONf_plane_restr0.0012021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7509-2.79830.27491750.1823156887
2.7983-2.84910.28191820.1828163990
2.8491-2.90380.27641840.1843166190
2.9038-2.9630.22451810.1727163090
2.963-3.02730.25351850.1718166190
3.0273-3.09760.25761800.1632162490
3.0976-3.17490.22471820.1629163690
3.1749-3.26060.23411840.1494165290
3.2606-3.35630.24011820.1415163990
3.3563-3.46440.18761830.1355164590
3.4644-3.58780.19781840.1307165790
3.5878-3.7310.18471810.1275163390
3.731-3.90020.17541840.12165590
3.9002-4.1050.16561830.1118164590
4.105-4.36090.15611840.1082165990
4.3609-4.69560.13771850.1055166290
4.6956-5.16430.13751820.1185163490
5.1643-5.90290.16861840.1386165690
5.9029-7.40470.18921850.1598166990
7.4047-24.94320.16211860.136167088

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