+Open data
-Basic information
Entry | Database: PDB / ID: 1cd9 | ||||||
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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 / 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 / positive regulation of peptidyl-tyrosine phosphorylation / 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 / 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 / MIRAS / Resolution: 2.8 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 | 1cd9.cif.gz | 159.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cd9.ent.gz | 128 KB | Display | PDB format |
PDBx/mmJSON format | 1cd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cd9_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 1cd9_full_validation.pdf.gz | 490.4 KB | Display | |
Data in XML | 1cd9_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 1cd9_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/1cd9 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/1cd9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.: 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 | 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 | #4: Water | ChemComp-HOH / | |
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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 7.50 |
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: BENT MIRROR |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: X-PLOR WAS ALSO USED
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Displacement parameters | Biso mean: 42.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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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 |