+Open data
-Basic information
Entry | Database: PDB / ID: 1m6b | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the HER3 (ERBB3) Extracellular Domain | |||||||||
Components | Receptor protein-tyrosine kinase erbB-3 | |||||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / tyrosine kinase / cell surface receptor / immunity | |||||||||
Function / homology | Function and homology information neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / growth factor binding / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / Schwann cell development / negative regulation of signal transduction / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / myelination / Downregulation of ERBB2:ERBB3 signaling / neurogenesis / SHC1 events in ERBB2 signaling / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / regulation of cell population proliferation / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / apical plasma membrane / protein heterodimerization activity / phosphorylation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | |||||||||
Authors | Leahy, D.J. / Cho, H.-S. | |||||||||
Citation | Journal: Science / Year: 2002 Title: Structure of the extracellular region of HER3 reveals an interdomain tether. Authors: Cho, H.S. / Leahy, D.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m6b.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m6b.ent.gz | 188.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6b ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6b | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 68376.547 Da / Num. of mol.: 2 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSGHV0 / Cell line (production host): LEC1 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): OVARY CELLS References: UniProt: P21860, receptor protein-tyrosine kinase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: pH 9.0, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
---|---|
Detector | Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 54360 / Num. obs: 48669 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % possible obs: 96.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 79.2 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.867 / SU B: 14.96 / SU ML: 0.301 / SU Rfree: 0.341 / Cross valid method: THROUGHOUT / ESU R: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.631 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|