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Yorodumi- PDB-3u7u: Crystal structure of extracellular region of human epidermal grow... -
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Basic information
| Entry | Database: PDB / ID: 3u7u | ||||||
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| Title | Crystal structure of extracellular region of human epidermal growth factor receptor 4 in complex with neuregulin-1 beta | ||||||
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Keywords | TRANSFERASE/TRANSFERASE REGULATOR / signaling protein / TRANSFERASE-TRANSFERASE REGULATOR COMPLEX / Glycosylation | ||||||
| Function / homology | Function and homology informationERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / activation of transmembrane receptor protein tyrosine kinase activity / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation ...ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / activation of transmembrane receptor protein tyrosine kinase activity / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation / neuregulin receptor activity / cardiac muscle tissue regeneration / negative regulation of secretion / endocardial cell differentiation / negative regulation of neuron migration / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / neural crest cell development / mitochondrial fragmentation involved in apoptotic process / cardiac muscle cell myoblast differentiation / cell communication / mammary gland epithelial cell differentiation / PI3K events in ERBB4 signaling / cardiac muscle cell differentiation / peripheral nervous system development / embryonic pattern specification / GABA receptor binding / transmembrane receptor protein tyrosine kinase activator activity / chemorepellent activity / ventricular trabecula myocardium morphogenesis / ErbB-3 class receptor binding / mammary gland development / positive regulation of protein localization to cell surface / neural crest cell migration / ERBB signaling pathway / epidermal growth factor receptor binding / epidermal growth factor receptor activity / negative regulation of cardiac muscle cell apoptotic process / positive regulation of tyrosine phosphorylation of STAT protein / ERBB2 Activates PTK6 Signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of postsynaptic neurotransmitter receptor internalization / ERBB2-ERBB3 signaling pathway / ERBB2 Regulates Cell Motility / nickel cation binding / protein tyrosine kinase activator activity / Signaling by ERBB4 / Long-term potentiation / PI3K events in ERBB2 signaling / mammary gland alveolus development / SHC1 events in ERBB4 signaling / cell fate commitment / activation of protein kinase B activity / cell surface receptor signaling pathway via JAK-STAT / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Nuclear signaling by ERBB4 / positive regulation of cardiac muscle cell proliferation / synapse assembly / lactation / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / Downregulation of ERBB4 signaling / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / regulation of cell migration / cellular response to epidermal growth factor stimulus / peptidyl-tyrosine phosphorylation / cytokine activity / positive regulation of epithelial cell proliferation / transcription coregulator activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / neuromuscular junction / positive regulation of protein-containing complex assembly / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / brain development / postsynaptic density membrane / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / GABA-ergic synapse / Downregulation of ERBB2 signaling / integrin binding / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / nervous system development / PIP3 activates AKT signaling / heart development / protein autophosphorylation / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.03 Å | ||||||
Authors | Liu, P. / Cleveland IV, T.E. / Bouyain, S. / Longo, P.A. / Leahy, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012Title: A single ligand is sufficient to activate EGFR dimers. Authors: Liu, P. / Cleveland, T.E. / Bouyain, S. / Byrne, P.O. / Longo, P.A. / Leahy, D.J. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 3u7u.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb3u7u.ent.gz | 1.2 MB | Display | PDB format |
| PDBx/mmJSON format | 3u7u.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 3u7u_validation.pdf.gz | 553.2 KB | Display | wwPDB validaton report |
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| Full document | 3u7u_full_validation.pdf.gz | 618 KB | Display | |
| Data in XML | 3u7u_validation.xml.gz | 133.5 KB | Display | |
| Data in CIF | 3u7u_validation.cif.gz | 180.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/3u7u ftp://data.pdbj.org/pub/pdb/validation_reports/u7/3u7u | HTTPS FTP |
-Related 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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| 3 | ![]()
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| 4 | ![]()
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| 5 | ![]()
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| 6 | ![]()
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| Unit cell |
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Components
| #1: Protein | Mass: 68735.508 Da / Num. of mol.: 6 / Fragment: Extracellular region (UNP Residues 26-640) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Plasmid: pSGHV0 / Production host: ![]() References: UniProt: Q15303, receptor protein-tyrosine kinase #2: Protein | Mass: 6196.122 Da / Num. of mol.: 6 / Fragment: EGF-like domain (UNP Residues 230-284) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRG1 / Plasmid: pET32 / Production host: ![]() #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 3.09 Å3/Da / Density % sol: 60.14 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, Mg(OAc)2, MES pH6.0, Hampton Silver Bullet, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
| Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98011 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection | Resolution: 3.03→50 Å / Num. all: 104051 / Num. obs: 104051 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 93.35 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell |
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-Phasing
| Phasing | Method: molecular replacement |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTREIS 1MOX AND 2AHX Resolution: 3.03→49.63 Å / Cor.coef. Fo:Fc: 0.9316 / Cor.coef. Fo:Fc free: 0.9044 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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| Displacement parameters | Biso mean: 91 Å2
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| Refine analyze | Luzzati coordinate error obs: 0.544 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.03→49.63 Å
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| Refine LS restraints |
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| LS refinement shell | Resolution: 3.03→3.11 Å / Total num. of bins used: 20
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
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