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- PDB-1cd9: 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1cd9
Title2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR
Components
  • PROTEIN (G-CSF RECEPTOR)
  • PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
KeywordsCYTOKINE / CLASS1 CYTOKINE / HEMATOPOIETIC RECEPTOR / SIGNAL TRANSDUCTION
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 / Other interleukin signaling ...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 / Other interleukin signaling / positive regulation of actin filament polymerization / cellular response to cytokine stimulus / Interleukin-10 signaling / Signaling by CSF3 (G-CSF) / neutrophil chemotaxis / endocytic vesicle lumen / lysosomal lumen / cytokine activity / growth factor activity / Inactivation of CSF3 (G-CSF) signaling / cytokine-mediated signaling pathway / endocytic vesicle membrane / cellular response to lipopolysaccharide / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / immune response / positive regulation of cell population proliferation / enzyme binding / 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 ...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 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsAritomi, M. / Kunishima, N. / Okamoto, T. / Kuroki, R. / Ota, Y. / Morikawa, K.
CitationJournal: Nature / Year: 1999
Title: Atomic structure of the GCSF-receptor complex showing a new cytokine-receptor recognition scheme.
Authors: Aritomi, M. / Kunishima, N. / Okamoto, T. / Kuroki, R. / Ota, Y. / Morikawa, K.
History
DepositionMar 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
B: PROTEIN (G-CSF RECEPTOR)
C: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
D: PROTEIN (G-CSF RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9966
Polymers86,5544
Non-polymers4422
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.467, 125.467, 372.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.78691, 0.61141, 0.08336), (0.61301, -0.79004, 0.00779), (0.07062, 0.04497, -0.99649)-22.31002, 32.9952, 251.97295
2given(0.86348, 0.48097, 0.1519), (0.48178, -0.87564, 0.0339), (0.14931, 0.04391, -0.98781)-31.65583, 38.74764, 247.10971

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Components

#1: Protein PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR) / G-CSF


Mass: 18816.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: EXTRACELLULAR / Production host: Escherichia coli (E. coli) / References: UniProt: P09919
#2: Protein PROTEIN (G-CSF RECEPTOR) / G-CSF-R


Mass: 24460.264 Da / Num. of mol.: 2 / Fragment: CRH REGION (BN DOMAIN:D1-108, BC DOMAIN:D109-215)
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATION AT B10 / Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: CELLULAR MEMBRANE / Cell line (production host): SF-9 / Cellular location (production host): NUCLEUS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40223
#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.: 2
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.: 260 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: unknown / Details: manuscript in preparation

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: BENT MIRROR
RadiationMonochromator: SILICON CRYSTAL / 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: 35565 / % possible obs: 95.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. measured all: 169036

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: X-PLOR WAS ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.319 510 1.4 %RANDOM
Rwork0.237 ---
all-35277 --
obs-35277 95.7 %-
Displacement parametersBiso mean: 42.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 28 260 6080
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_scangle_it3
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.3
X-RAY DIFFRACTIONp_multtor_nbd0.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3
X-RAY DIFFRACTIONp_planar_tor7
X-RAY DIFFRACTIONp_staggered_tor15
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 35565 / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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