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- PDB-2d9q: Crystal Structure of the Human GCSF-Receptor Signaling Complex -

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Basic information

Entry
Database: PDB / ID: 2d9q
TitleCrystal Structure of the Human GCSF-Receptor Signaling Complex
Components
  • CSF3
  • Granulocyte colony-stimulating factor receptor
KeywordsSIGNALING PROTEIN/CYTOKINE / CYTOKINE / LIGAND-RECEPTOR COMPLEX / SIGNALING PROTEIN-CYTOKINE COMPLEX
Function / homology
Function and homology information


granulocyte colony-stimulating factor binding / granulocyte colony-stimulating factor receptor binding / regulation of myeloid cell differentiation / granulocyte colony-stimulating factor signaling pathway / positive regulation of myeloid cell differentiation / granulocyte differentiation / amelogenesis / regulation of actin filament organization / cytokine receptor activity / positive regulation of actin filament polymerization ...granulocyte colony-stimulating factor binding / granulocyte colony-stimulating factor receptor binding / regulation of myeloid cell differentiation / granulocyte colony-stimulating factor signaling pathway / positive regulation of myeloid cell differentiation / granulocyte differentiation / amelogenesis / regulation of actin filament organization / cytokine receptor activity / positive regulation of actin filament polymerization / Other interleukin signaling / cellular response to cytokine stimulus / cytokine binding / Interleukin-10 signaling / Signaling by CSF3 (G-CSF) / endocytic vesicle lumen / neutrophil chemotaxis / lysosomal lumen / cytokine activity / growth factor activity / Inactivation of CSF3 (G-CSF) signaling / cytokine-mediated signaling pathway / defense response / Transcriptional regulation of granulopoiesis / positive regulation of peptidyl-tyrosine phosphorylation / endocytic vesicle membrane / signaling receptor activity / cellular response to lipopolysaccharide / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / immune response / lysosomal membrane / external side of plasma membrane / positive regulation of cell population proliferation / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
GCSF/MGF / Granulocyte colony-stimulating factor / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. ...GCSF/MGF / Granulocyte colony-stimulating factor / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / : / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Granulocyte colony-stimulating factor / Granulocyte colony-stimulating factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTamada, T. / Kuroki, R.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex
Authors: Tamada, T. / Honjo, E. / Maeda, Y. / Okamoto, T. / Ishibashi, M. / Tokunaga, M. / Kuroki, R.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005
Title: Crystallization of a 2:2 complex of granulocyte-colony stimulating factor (GCSF) with the ligand-binding region of the GCSF receptor
Authors: Honjo, E. / Tamada, T. / Meada, Y. / Koshiba, T. / Matsukura, Y. / Okamoto, T. / Ishibashi, M. / Tokunaga, M. / Kuroki, R.
#2: Journal: Biochemistry / Year: 2004
Title: Thermodynamic analysis of the activation mechanism of the GCSF receptor induced by ligand binding
Authors: Mine, S. / Koshiba, T. / Honjo, E. / Okamoto, T. / Tamada, T. / Maeda, Y. / Matsukura, Y. / Horie, A. / Ishibashi, M. / Sato, M. / Azuma, M. / Tokunaga, M. / Nitta, K. / Kuroki, R.
History
DepositionDec 12, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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 / _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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CSF3
B: Granulocyte colony-stimulating factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8203
Polymers53,3952
Non-polymers4241
Water25214
1
A: CSF3
B: Granulocyte colony-stimulating factor receptor
hetero molecules

A: CSF3
B: Granulocyte colony-stimulating factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6396
Polymers106,7914
Non-polymers8492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)134.777, 134.777, 105.468
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CSF3 / Granulocyte colony stimulating factor / GCSF


Mass: 18685.564 Da / Num. of mol.: 1 / Fragment: residues 1-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09919
#2: Protein Granulocyte colony-stimulating factor receptor / G-CSF-R / CD114 antigen / GCSF-R


Mass: 34709.715 Da / Num. of mol.: 1 / Fragment: Ig-CRH DOMAIN / Mutation: C79S, C164S, C229S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99062
#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.: 1
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)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.17 Å3/Da / Density % sol: 76.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2M ammonium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2003
RadiationMonochromator: 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. obs: 25214 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2129 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
SHARPphasing
PHASERphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CD9

1cd9


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.388 / SU ML: 0.302 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28445 1264 5 %RANDOM
Rwork0.25145 ---
all0.25311 23837 --
obs0.25311 23837 91.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 68.031 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å21.66 Å20 Å2
2--3.32 Å20 Å2
3----4.98 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 0 28 14 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0213738
X-RAY DIFFRACTIONr_bond_other_d0.0010.023371
X-RAY DIFFRACTIONr_angle_refined_deg2.9751.985105
X-RAY DIFFRACTIONr_angle_other_deg1.18237893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7485464
X-RAY DIFFRACTIONr_chiral_restr0.1430.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024085
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02660
X-RAY DIFFRACTIONr_nbd_refined0.3140.31037
X-RAY DIFFRACTIONr_nbd_other0.2960.34287
X-RAY DIFFRACTIONr_nbtor_other0.1260.52406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.5169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.54
X-RAY DIFFRACTIONr_mcbond_it2.08922340
X-RAY DIFFRACTIONr_mcangle_it3.66733773
X-RAY DIFFRACTIONr_scbond_it1.87821398
X-RAY DIFFRACTIONr_scangle_it3.20931332
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 60
Rwork0.439 1494

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