+Open data
-Basic information
Entry | Database: PDB / ID: 6mok | ||||||
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Title | Dimeric DARPin A_distance_R7 complex with EpoR | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / DARPin / complex / receptor | ||||||
Function / homology | Function and homology information erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | synthetic construct (others) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.101 Å | ||||||
Authors | Jude, K.M. / Mohan, K. / Garcia, K.C. / Guo, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2019 Title: Topological control of cytokine receptor signaling induces differential effects in hematopoiesis. Authors: Mohan, K. / Ueda, G. / Kim, A.R. / Jude, K.M. / Fallas, J.A. / Guo, Y. / Hafer, M. / Miao, Y. / Saxton, R.A. / Piehler, J. / Sankaran, V.G. / Baker, D. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mok.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mok.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 6mok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/6mok ftp://data.pdbj.org/pub/pdb/validation_reports/mo/6mok | HTTPS FTP |
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-Related structure data
Related structure data | 6moeC 6mofC 6mogC 6mohC 6moiC 6mojC 6molC 1ernS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/623 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30736.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 25129.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPOR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19235 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00001 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 5.101→46.79 Å / Num. obs: 4205 / % possible obs: 98.38 % / Redundancy: 9.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.03905 / Rrim(I) all: 0.123 / Net I/σ(I): 9.92 |
Reflection shell | Resolution: 5.101→5.283 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.75 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 395 / CC1/2: 0.585 / Rpim(I) all: 0.884 / % possible all: 98.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: predicted model, 1ERN Resolution: 5.101→46.79 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.893 / SU B: 146.123 / SU ML: 1.434 / Cross valid method: FREE R-VALUE / ESU R Free: 1.576
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 434.475 Å2
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Refinement step | Cycle: 1 / Resolution: 5.101→46.79 Å
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Refine LS restraints |
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