[English] 日本語
Yorodumi- PDB-3u7u: Crystal structure of extracellular region of human epidermal grow... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u7u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of extracellular region of human epidermal growth factor receptor 4 in complex with neuregulin-1 beta | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/TRANSFERASE REGULATOR / signaling protein / TRANSFERASE-TRANSFERASE REGULATOR COMPLEX / Glycosylation | ||||||
Function / homology | Function and homology information ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation ...ERBB3 signaling pathway / positive regulation of peptidyl-tyrosine autophosphorylation / sequestering of metal ion / establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / ventricular cardiac muscle cell differentiation / positive regulation of striated muscle cell differentiation / neuregulin receptor activity / negative regulation of secretion / cardiac muscle tissue regeneration / endocardial cell differentiation / animal organ development / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / mitochondrial fragmentation involved in apoptotic process / neural crest cell development / cardiac muscle cell myoblast differentiation / embryonic pattern specification / mammary gland development / GABA receptor binding / cell communication / PI3K events in ERBB4 signaling / cardiac muscle cell differentiation / mammary gland epithelial cell differentiation / chemorepellent activity / ventricular trabecula myocardium morphogenesis / ErbB-3 class receptor binding / positive regulation of protein localization to cell surface / regulation of postsynaptic neurotransmitter receptor internalization / activation of transmembrane receptor protein tyrosine kinase activity / neural crest cell migration / epidermal growth factor receptor activity / ERBB signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of cardiac muscle cell apoptotic process / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / protein tyrosine kinase activator activity / transmembrane receptor protein tyrosine kinase activator activity / ERBB2-ERBB3 signaling pathway / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / cell surface receptor signaling pathway via JAK-STAT / Long-term potentiation / PI3K events in ERBB2 signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / SHC1 events in ERBB4 signaling / cell fate commitment / mammary gland alveolus development / positive regulation of cardiac muscle cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / GABA-ergic synapse / Nuclear signaling by ERBB4 / positive regulation of tyrosine phosphorylation of STAT protein / Signaling by ERBB2 / synapse assembly / cellular response to epidermal growth factor stimulus / lactation / activation of protein kinase B activity / GRB2 events in ERBB2 signaling / regulation of cell migration / transmembrane receptor protein tyrosine kinase activity / Downregulation of ERBB4 signaling / SHC1 events in ERBB2 signaling / positive regulation of cell adhesion / Downregulation of ERBB2:ERBB3 signaling / neurogenesis / basal plasma membrane / cytokine activity / Signaling by ERBB2 TMD/JMD mutants / transcription coregulator activity / positive regulation of receptor signaling pathway via JAK-STAT / postsynaptic density membrane / growth factor activity / positive regulation of protein-containing complex assembly / wound healing / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / cell migration / PIP3 activates AKT signaling / heart development / presynaptic membrane / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / postsynaptic membrane / Estrogen-dependent gene expression / protein autophosphorylation 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: 2012 Title: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3u7u.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
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 |
---|---|---|---|---|
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
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-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: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1 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: Escherichia coli (E. coli) / References: UniProt: Q96IB3, UniProt: Q02297*PLUS #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.14 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.544 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.03→49.63 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.03→3.11 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|