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Open data
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Basic information
Entry | Database: PDB / ID: 1pgr | ||||||
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Title | 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR | ||||||
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![]() | CYTOKINE / CLASS1 CYTOKINE / HEMATOPOIETIC RECEPTOR / SIGNAL TRANSDUCTION | ||||||
Function / homology | ![]() 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 / 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 / cellular response to lipopolysaccharide / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aritomi, M. / Kunishima, N. / Okamoto, T. / Kuroki, R. / Ota, Y. / Morikawa, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.3 KB | Display | ![]() |
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PDB format | ![]() | 234 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.7 KB | Display | ![]() |
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Full document | ![]() | 541.1 KB | Display | |
Data in XML | ![]() | 54.6 KB | Display | |
Data in CIF | ![]() | 74 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cd9C ![]() 1igrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |