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- PDB-4exp: Structure of mouse Interleukin-34 in complex with mouse FMS -

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Basic information

Entry
Database: PDB / ID: 4exp
TitleStructure of mouse Interleukin-34 in complex with mouse FMS
Components
  • Interleukin-34
  • Macrophage colony-stimulating factor 1 receptor
KeywordsCYTOKINE/TRANSFERASE / extended 4-helix bundle / immunoglobunin / beta-sandwich / CYTOKINE-TRANSFERASE complex
Function / homology
Function and homology information


Other interleukin signaling / macrophage colony-stimulating factor receptor binding / forebrain neuron differentiation / macrophage colony-stimulating factor receptor activity / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / cell-cell junction maintenance / microglial cell proliferation ...Other interleukin signaling / macrophage colony-stimulating factor receptor binding / forebrain neuron differentiation / macrophage colony-stimulating factor receptor activity / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / cell-cell junction maintenance / microglial cell proliferation / interleukin-34-mediated signaling pathway / positive regulation of macrophage differentiation / olfactory bulb development / host-mediated activation of viral process / ruffle organization / positive regulation of monocyte differentiation / positive regulation of macrophage proliferation / regulation of bone resorption / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of macrophage chemotaxis / cytokine binding / cellular response to cytokine stimulus / positive regulation of oligodendrocyte differentiation / positive regulation of chemokine production / transmembrane receptor protein tyrosine kinase activity / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / peptidyl-tyrosine phosphorylation / response to ischemia / cytokine activity / regulation of actin cytoskeleton organization / growth factor activity / receptor protein-tyrosine kinase / positive regulation of protein phosphorylation / regulation of cell shape / protein autophosphorylation / protein tyrosine kinase activity / protein phosphatase binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / inflammatory response / negative regulation of cell population proliferation / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular space / nucleoplasm / ATP binding / membrane / plasma membrane
Similarity search - Function
Interleukin-34 / Interleukin-34 / Interleukin-34 superfamily / Interleukin 34 / Macrophage colony-stimulating factor 1 receptor / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; / Immunoglobulin ...Interleukin-34 / Interleukin-34 / Interleukin-34 superfamily / Interleukin 34 / Macrophage colony-stimulating factor 1 receptor / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1 receptor / Interleukin-34
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, H. / Leo, C. / Chen, X. / Wong, B.R. / Williams, L.T. / Lin, H. / He, X.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: The mechanism of shared but distinct CSF-1R signaling by the non-homologous cytokines IL-34 and CSF-1.
Authors: Liu, H. / Leo, C. / Chen, X. / Wong, B.R. / Williams, L.T. / Lin, H. / He, X.
History
DepositionApr 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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: Interleukin-34
X: Macrophage colony-stimulating factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6566
Polymers51,7712
Non-polymers8854
Water3,567198
1
A: Interleukin-34
X: Macrophage colony-stimulating factor 1 receptor
hetero molecules

A: Interleukin-34
X: Macrophage colony-stimulating factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,31212
Polymers103,5434
Non-polymers1,7708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_754-x+2,y,-z-1/21
Unit cell
Length a, b, c (Å)44.713, 135.340, 203.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Interleukin-34 / IL-34


Mass: 20547.934 Da / Num. of mol.: 1 / Fragment: UNP residues 21-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il34 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q8R1R4
#2: Protein Macrophage colony-stimulating factor 1 receptor / FMS / CSF-1 receptor / CSF-1-R / CSF-1R / M-CSF-R / Proto-oncogene c-Fms


Mass: 31223.330 Da / Num. of mol.: 1 / Fragment: UNP residues 20-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csf1r, Csfmr, Fms / Cell line (production host): HEK / Production host: Homo sapiens (human)
References: UniProt: P09581, receptor protein-tyrosine kinase
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG3000, 0.1 M sodium acetate, 0.2 M lithium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2009
RadiationMonochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 15606 / Num. obs: 15606 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1503 / % possible all: 96.5

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Processing

Software
NameClassification
HKL-3000data collection
PHASERphasing
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4EXN AND 3EJJ

4exn

3ejj


Resolution: 2.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 772 4.9 %RANDOM
Rwork0.2485 14834 --
obs-15606 99.3 %-
Solvent computationBsol: 55.4216 Å2
Displacement parametersBiso max: 150.62 Å2 / Biso mean: 85.7185 Å2 / Biso min: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.219 Å20 Å20 Å2
2---14.158 Å20 Å2
3---16.377 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 56 198 3838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.271
LS refinement shellResolution: 2.8→2.91 Å /
Num. reflection% reflection
Rfree80 -
obs1503 96.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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