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- PDB-5lxf: Crystal structure of the human Macrophage Colony Stimulating Fact... -

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Basic information

Entry
Database: PDB / ID: 5lxf
TitleCrystal structure of the human Macrophage Colony Stimulating Factor M- CSF_C31S variant
ComponentsMacrophage colony-stimulating factor 1
KeywordsSIGNALING PROTEIN / Drug design / rational protein engineering / receptor tyrosine kinase / osteoporosis
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 / macrophage homeostasis / monocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / positive regulation of odontogenesis of dentin-containing tooth ...regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / monocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / mammary duct terminal end bud growth / microglial cell proliferation / positive regulation of macrophage derived foam cell differentiation / positive regulation of macrophage differentiation / positive regulation of mononuclear cell proliferation / myeloid leukocyte migration / neutrophil homeostasis / positive regulation of multicellular organism growth / positive regulation of monocyte differentiation / positive regulation of osteoclast differentiation / positive regulation of Ras protein signal transduction / branching involved in mammary gland duct morphogenesis / positive regulation of cell-matrix adhesion / Other interleukin signaling / positive regulation of macrophage chemotaxis / Interleukin-10 signaling / monocyte differentiation / macrophage differentiation / regulation of ossification / positive regulation of protein kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / homeostasis of number of cells within a tissue / positive regulation of protein metabolic process / osteoclast differentiation / cytokine activity / response to ischemia / Post-translational protein phosphorylation / growth factor activity / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Ras protein signal transduction / nuclear body / positive regulation of cell migration / inflammatory response / endoplasmic reticulum lumen / 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 / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / 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 Å
AuthorsShahar, A. / Papo, N. / Zarivach, R. / Kosloff, M. / Bakhman, A. / Rosenfeld, L. / Zur, Y. / Levaot, N.
CitationJournal: Biochem. J. / Year: 2017
Title: Engineering a monomeric variant of macrophage colony-stimulating factor (M-CSF) that antagonizes the c-FMS receptor.
Authors: Zur, Y. / Rosenfeld, L. / Bakhman, A. / Ilic, S. / Hayun, H. / Shahar, A. / Akabayov, B. / Kosloff, M. / Levaot, N. / Papo, N.
History
DepositionSep 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)42,7092
Polymers42,7092
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-9 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.271, 65.471, 158.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Macrophage colony-stimulating factor 1 / MCSF / Lanimostim


Mass: 21354.736 Da / Num. of mol.: 2 / Mutation: C31S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P09603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.03M Bis-Tris pH 6.5; 0.17M Mg Formate; 16.67% PEG 3350; 0.07M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→39.66 Å / Num. obs: 20774 / % possible obs: 95.1 % / Redundancy: 8.7 % / Rpim(I) all: 0.025 / Net I/σ(I): 26.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1 / CC1/2: 0.727 / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UF2

3uf2


Resolution: 2→39.66 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1027 4.94 %Random selection
Rwork0.1885 ---
obs0.1917 20774 85.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 0 261 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092491
X-RAY DIFFRACTIONf_angle_d1.1763367
X-RAY DIFFRACTIONf_dihedral_angle_d7.0732147
X-RAY DIFFRACTIONf_chiral_restr0.062375
X-RAY DIFFRACTIONf_plane_restr0.006437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10540.331810.23051417X-RAY DIFFRACTION44
2.1054-2.23730.26251190.24362256X-RAY DIFFRACTION70
2.2373-2.41010.36911510.23612863X-RAY DIFFRACTION89
2.4101-2.65260.3011500.21363158X-RAY DIFFRACTION96
2.6526-3.03630.27991800.20143265X-RAY DIFFRACTION99
3.0363-3.8250.2541700.17543307X-RAY DIFFRACTION99
3.825-41.14510.19441760.15953481X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04050.1210.42022.32293.42475.07590.17440.0185-0.26390.44290.1031-0.15080.8822-0.1941-0.11980.111-0.04120.02240.1488-0.02360.2088-5.4147-16.626811.9395
20.4681-0.49310.17540.5141-0.18740.0644-0.3831-0.05890.17160.22770.0391-0.1091-0.77920.1686-0.16090.6325-0.0153-0.08490.1349-0.0190.269-4.32381.320125.5752
32.6573-1.6681.32164.52993.15845.27160.3013-0.61490.42481.3899-0.39820.9586-0.6026-0.73870.17020.6650.05890.03530.6894-0.30560.5359-17.46723.680510.5941
43.9821-1.27141.86292.0193-0.02915.1636-0.45610.19450.07950.14280.3269-0.2063-0.92810.71630.17670.2946-0.09950.02570.2341-0.05960.2272-0.9362-3.988713.6565
50.84820.2338-0.28160.10560.12961.02780.06390.114-0.02010.01430.1864-0.0382-0.04210.39080.13170.026-0.05660.03250.3281-0.14920.2491.9602-12.159111.2943
64.12650.0572-0.92540.22790.43311.077-0.20060.83571.2021-0.8986-0.0064-0.9837-1.69630.10360.01530.8664-0.1206-0.0680.4110.1140.5167-6.77113.63430.0327
70.48940.28270.51291.90110.91444.2973-0.11690.04910.22020.0033-0.19220.2522-1.0163-0.38930.09770.25220.0382-0.0330.2184-0.04290.2593-11.3795-3.961410.5809
82.56170.35210.67331.5734-2.64186.56140.19830.0024-0.48590.5571-0.0031-0.33160.69350.70750.01050.59250.1519-0.11240.263-0.04780.366410.3604-16.331646.9336
97.2825-2.11310.08952.46633.7919.2043-0.4160.57010.7987-0.42630.3654-0.3587-1.65490.69560.00540.4733-0.1581-0.03170.4757-0.02180.18433.9015-1.675428.2453
101.767-0.69930.69611.7544-0.22883.6801-0.1074-0.08860.3450.0245-0.0841-0.2918-0.07040.20640.03770.29440.0786-0.02580.0943-0.03580.28918.93935.624846.9958
113.85-0.07762.96411.09141.1674.51190.198-0.2758-0.04220.5636-0.0328-0.21430.4998-0.1249-0.120.39990.0557-0.02780.1286-0.02650.28175.7948-3.557751.2563
125.26281.9443-0.97471.26060.47033.2614-0.0784-0.14910.2930.0732-0.0780.281-0.0475-0.47860.2170.26830.0508-0.00330.1597-0.02710.2018-5.3914-10.830537.4545
131.7246-0.81980.56651.105-1.66032.89720.0857-0.0876-0.11820.85090.0273-0.17560.0893-0.07470.09180.51250.0266-0.03840.1012-0.00840.26711.969-15.10847.8893
141.13190.25870.79932.07830.0661.2943-0.0063-0.1009-0.00650.62460.1375-0.26380.2270.2204-0.00540.43510.0859-0.09190.1897-0.04210.256210.3242-1.41252.8353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 45 )
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 102 )
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 147 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 24 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 31 )
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 45 )
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 63 )
12X-RAY DIFFRACTION12chain 'B' and (resid 64 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 150 )

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