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Yorodumi- PDB-1eer: CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPT... -
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-Basic information
Entry | Database: PDB / ID: 1eer | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPTOR AT 1.9 ANGSTROMS | ||||||
Components |
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Keywords | COMPLEX (CYTOKINE/RECEPTOR) / ERYTHROPOIETIN / ERYTHROPOIETIN RECEPTOR / SIGNAL TRANSDUCTION / HEMATOPOIETIC CYTOKINE / CYTOKINE RECEPTOR CLASS 1 / COMPLEX (CYTOKINE-RECEPTOR) / COMPLEX (CYTOKINE-RECEPTOR) complex | ||||||
Function / homology | Function and homology information nucleate erythrocyte development / negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / negative regulation of cation channel activity / erythropoietin-mediated signaling pathway / myeloid cell apoptotic process / hemoglobin biosynthetic process / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / negative regulation of calcium ion transport into cytosol ...nucleate erythrocyte development / negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / negative regulation of cation channel activity / erythropoietin-mediated signaling pathway / myeloid cell apoptotic process / hemoglobin biosynthetic process / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / negative regulation of calcium ion transport into cytosol / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / cellular hyperosmotic response / response to vitamin A / positive regulation of Ras protein signal transduction / blood circulation / Regulation of gene expression by Hypoxia-inducible Factor / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / response to testosterone / protein kinase activator activity / response to dexamethasone / positive regulation of activated T cell proliferation / erythrocyte maturation / hemopoiesis / decidualization / response to axon injury / response to hyperoxia / response to electrical stimulus / Erythropoietin activates RAS / positive regulation of tyrosine phosphorylation of STAT protein / response to salt stress / embryo implantation / positive regulation of neuron differentiation / response to interleukin-1 / erythrocyte differentiation / cytokine activity / acute-phase response / brain development / hormone activity / cytokine-mediated signaling pathway / positive regulation of neuron projection development / response to estrogen / heart development / cell body / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å | ||||||
Authors | Syed, R.S. / Li, C. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Efficiency of signalling through cytokine receptors depends critically on receptor orientation. Authors: Syed, R.S. / Reid, S.W. / Li, C. / Cheetham, J.C. / Aoki, K.H. / Liu, B. / Zhan, H. / Osslund, T.D. / Chirino, A.J. / Zhang, J. / Finer-Moore, J. / Elliott, S. / Sitney, K. / Katz, B.A. / ...Authors: Syed, R.S. / Reid, S.W. / Li, C. / Cheetham, J.C. / Aoki, K.H. / Liu, B. / Zhan, H. / Osslund, T.D. / Chirino, A.J. / Zhang, J. / Finer-Moore, J. / Elliott, S. / Sitney, K. / Katz, B.A. / Matthews, D.J. / Wendoloski, J.J. / Egrie, J. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eer.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eer.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 1eer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1eer ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eer | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18471.289 Da / Num. of mol.: 1 / Mutation: N24K, N38K, N83K, P121N, P122S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01588 | ||
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#2: Protein | Mass: 25186.449 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN / Mutation: N52Q, N164Q, A211E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P19235 #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 49480 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.377 / % possible all: 82.9 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Num. measured all: 251681 / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 23.5 Å2 |
Reflection shell | *PLUS % possible obs: 82.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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