+Open data
-Basic information
Entry | Database: PDB / ID: 1pgr | ||||||
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Title | 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR | ||||||
Components |
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Keywords | CYTOKINE / 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 / immunoglobulin mediated immune response / endocytic vesicle lumen / Signaling by CSF3 (G-CSF) / lysosomal lumen / neutrophil chemotaxis / cytokine activity / growth factor activity / Inactivation of CSF3 (G-CSF) signaling / cytokine-mediated signaling pathway / endocytic vesicle membrane / positive regulation of peptidyl-tyrosine phosphorylation / response to ethanol / cellular response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / immune response / external side of plasma membrane / 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 | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Aritomi, M. / Kunishima, N. / Okamoto, T. / Kuroki, R. / Ota, Y. / Morikawa, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pgr.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pgr.ent.gz | 234 KB | Display | PDB format |
PDBx/mmJSON format | 1pgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pgr ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pgr | HTTPS FTP |
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-Related structure data
Related structure data | 1cd9C 1igrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 18816.760 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: EXTRACELLULARGlossary of biology / Production host: Escherichia coli (E. coli) / References: UniProt: P09919 #2: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
Crystal grow | *PLUS Method: unknown / Details: manuscript in preparation |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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.
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Displacement parameters | Biso mean: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.64 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO |