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- PDB-3ejj: Structure of M-CSF bound to the first three domains of FMS -

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Basic information

Entry
Database: PDB / ID: 3ejj
TitleStructure of M-CSF bound to the first three domains of FMS
Components
  • Colony stimulating factor-1
  • Macrophage colony-stimulating factor 1 receptor
KeywordsCYTOKINE/SIGNALING PROTEIN / growth factor-receptor complex / receptor tyrosine kinase / cytokine / 4-helix bundle / ATP-binding / Glycoprotein / Immunoglobulin domain / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Proto-oncogene / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / CYTOKINE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of protein metabolic process => GO:0051247 / regulation of mononuclear cell proliferation / negative regulation of platelet formation / Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / positive regulation of astrocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis ...positive regulation of protein metabolic process => GO:0051247 / regulation of mononuclear cell proliferation / negative regulation of platelet formation / Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / positive regulation of astrocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / : / positive regulation of macrophage migration / developmental process involved in reproduction / macrophage colony-stimulating factor receptor activity / positive regulation of odontogenesis of dentin-containing tooth / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / positive regulation of microglial cell migration / regulation of macrophage migration / mammary duct terminal end bud growth / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / positive regulation of lymphocyte proliferation / cellular response to macrophage colony-stimulating factor stimulus / negative regulation of myotube differentiation / positive regulation of cell cycle G1/S phase transition / organic cyclic compound binding / positive regulation of myoblast proliferation / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / olfactory bulb development / positive regulation of mononuclear cell proliferation / myeloid leukocyte migration / dentate gyrus development / positive regulation of mononuclear cell migration / positive regulation of leukocyte proliferation / positive regulation by host of viral process / neutrophil homeostasis / ruffle organization / positive regulation of multicellular organism growth / positive regulation of monocyte differentiation / positive regulation of osteoclast differentiation / microglia development / positive regulation of Ras protein signal transduction / positive regulation of macrophage proliferation / positive regulation of cell motility / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / odontogenesis / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / neuron projection extension / negative regulation of epithelial cell differentiation / positive regulation of macrophage chemotaxis / cytokine binding / growth factor binding / cellular response to cytokine stimulus / regulation of MAPK cascade / monocyte differentiation / hemopoiesis / macrophage differentiation / regulation of ossification / positive regulation of protein kinase activity / positive regulation of bone mineralization / homeostasis of number of cells within a tissue / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of protein metabolic process / transmembrane receptor protein tyrosine kinase activity / ossification / osteoclast differentiation / cytokine activity / response to ischemia / axon guidance / regulation of actin cytoskeleton organization / microglial cell activation / growth factor activity / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of tumor necrosis factor production / cell body / regulation of cell shape / perikaryon / protein phosphatase binding / protein tyrosine kinase activity / Ras protein signal transduction / cell population proliferation / protein autophosphorylation / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / nuclear body / positive regulation of cell migration
Similarity search - Function
Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Macrophage colony-stimulating factor 1 receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain ...Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Macrophage colony-stimulating factor 1 receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1 / Macrophage colony-stimulating factor 1 receptor / Macrophage colony-stimulating factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, X. / Liu, H. / Focia, P.J. / Shim, A. / He, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of macrophage colony stimulating factor bound to FMS: diverse signaling assemblies of class III receptor tyrosine kinases.
Authors: Chen, X. / Liu, H. / Focia, P.J. / Shim, A.H. / He, X.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Colony stimulating factor-1
B: Colony stimulating factor-1
X: Macrophage colony-stimulating factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2905
Polymers68,4413
Non-polymers8492
Water11,782654
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.848, 158.848, 237.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11X-315-

HOH

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Components

#1: Protein Colony stimulating factor-1


Mass: 18194.328 Da / Num. of mol.: 2 / Fragment: M-CSF (UNP residues 36 to 180)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csf1 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3U395, UniProt: P07141*PLUS
#2: Protein Macrophage colony-stimulating factor 1 receptor / CSF-1-R / Fms proto-oncogene / c-fms


Mass: 32052.201 Da / Num. of mol.: 1 / Fragment: c-FMS (UNP residues 20 to 298)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csf1r, Csfmr, Fms / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P09581, receptor protein-tyrosine kinase
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O

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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: 4.23 Å3/Da / Density % sol: 70.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 12% PEG 3000, 0.1M Hepes, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9766 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 5, 2008
RadiationMonochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 44786 / Num. obs: 44786 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.9
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6957 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HMC

1hmc


Resolution: 2.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2247 -RANDOM
Rwork0.238 ---
all0.241 44786 --
obs0.241 44786 5 %-
Displacement parametersBiso mean: 73 Å2
Baniso -1Baniso -2Baniso -3
1--5.31 Å2-5.31 Å210.62 Å2
2--0.47 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 56 654 5213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.372 363 -
Rwork0.36 --
obs-6957 5 %

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