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

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Basic information

Entry
Database: PDB / ID: 1pgr
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 / cellular response to cytokine stimulus / positive regulation of actin filament polymerization / 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 / MOLECULAR REPLACEMENT / Resolution: 3.5 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: Version format compliance
Revision 1.3Aug 16, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)
E: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
F: PROTEIN (G-CSF RECEPTOR)
G: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
H: PROTEIN (G-CSF RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)173,1088
Polymers173,1088
Non-polymers00
Water00
1
A: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
B: PROTEIN (G-CSF RECEPTOR)
C: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
D: PROTEIN (G-CSF RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)86,5544
Polymers86,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
F: PROTEIN (G-CSF RECEPTOR)
G: PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
H: PROTEIN (G-CSF RECEPTOR)


Theoretical massNumber of molelcules
Total (without water)86,5544
Polymers86,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.725, 125.725, 373.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.78247, 0.61541, -0.09493), (0.61786, -0.78627, -0.00444), (-0.07737, -0.05518, -0.99547)-8.59733, 37.6754, 82.13613
2given(-0.80372, 0.59498, 0.00623), (0.59286, 0.79987, 0.09343), (0.05061, 0.07879, -0.99561)191.32515, -76.77528, 291.03754
3given(0.85916, 0.48712, -0.15671), (0.48907, -0.87178, -0.02855), (-0.15053, -0.05211, -0.98723)-6.19321, 57.74374, 90.00829
4given(-0.86706, 0.49754, 0.02553), (0.49592, 0.85708, 0.13954), (0.04755, 0.13365, -0.98989)200.76083, -73.60762, 288.21735

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Components

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


Mass: 18816.760 Da / Num. of mol.: 4
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.: 4 / Fragment: CRH REGION (BN DOMAIN:H1-108, BC DOMAIN:H109-215)
Source method: isolated from a genetically manipulated source
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
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 7.5
Crystal grow
*PLUS
Method: unknown / Details: manuscript in preparation

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Dec 1, 1997 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 26681 / % possible obs: 69.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.198
Reflection
*PLUS
Num. obs: 26690 / Num. measured all: 173168

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGR

1igr


Resolution: 3.5→8 Å / σ(F): 0
Details: RIGID-BODY REFINEMENT THE 107TH VALINES IN CHAINS B,D,F,H WERE REMOVED FOR THE RIGID-BODY REFINEMENT. INITIAL MODEL WAS OBTAINED BY A MOLECULAR REPLACEMENT OF 1IGR. A RIGID-BODY REFINEMENT ...Details: RIGID-BODY REFINEMENT THE 107TH VALINES IN CHAINS B,D,F,H WERE REMOVED FOR THE RIGID-BODY REFINEMENT. INITIAL MODEL WAS OBTAINED BY A MOLECULAR REPLACEMENT OF 1IGR. A RIGID-BODY REFINEMENT WAS APPLIED TO THE MODEL AS INDEPENDENT 12 GROUPS. FURTHER POSITIONAL OR B-FACTOR REFINEMENTS FOR INDIVIDUAL ATOMS WERE NOT APPLIED.
RfactorNum. reflection% reflection
Rwork0.317 --
obs-24595 69.8 %
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11424 0 0 0 11424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.5→3.64 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.335 3020 -
obs--69.8 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO

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