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Yorodumi- PDB-4p59: HER3 extracellular domain in complex with Fab fragment of MOR09825 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p59 | |||||||||
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Title | HER3 extracellular domain in complex with Fab fragment of MOR09825 | |||||||||
Components |
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Keywords | Signaling protein / immune system / Her3 receptor / therapeutic antibody / Fab fragment / anti-Her3 | |||||||||
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 / ERBB2 Activates PTK6 Signaling ...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 / ERBB2 Activates PTK6 Signaling / protein tyrosine kinase activator activity / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / Signaling by ERBB4 / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / motor neuron apoptotic process / ERBB2-ERBB3 signaling pathway / growth factor binding / Signaling by ERBB2 / lateral plasma membrane / neurogenesis / SHC1 events in ERBB2 signaling / negative regulation of signal transduction / Schwann cell development / basal plasma membrane / extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor protein tyrosine kinase signaling pathway / myelination / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Downregulation of ERBB2:ERBB3 signaling / Signaling by ERBB2 TMD/JMD mutants / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / wound healing / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / regulation of cell population proliferation / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / apical plasma membrane / protein heterodimerization activity / positive regulation of cell population proliferation / ubiquitin protein ligase binding / 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 / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | |||||||||
Authors | Sprague, E.R. | |||||||||
Citation | Journal: Cancer Res. / Year: 2013 Title: An antibody that locks HER3 in the inactive conformation inhibits tumor growth driven by HER2 or neuregulin. Authors: Garner, A.P. / Bialucha, C.U. / Sprague, E.R. / Garrett, J.T. / Sheng, Q. / Li, S. / Sineshchekova, O. / Saxena, P. / Sutton, C.R. / Chen, D. / Chen, Y. / Wang, H. / Liang, J. / Das, R. / ...Authors: Garner, A.P. / Bialucha, C.U. / Sprague, E.R. / Garrett, J.T. / Sheng, Q. / Li, S. / Sineshchekova, O. / Saxena, P. / Sutton, C.R. / Chen, D. / Chen, Y. / Wang, H. / Liang, J. / Das, R. / Mosher, R. / Gu, J. / Huang, A. / Haubst, N. / Zehetmeier, C. / Haberl, M. / Elis, W. / Kunz, C. / Heidt, A.B. / Herlihy, K. / Murtie, J. / Schuller, A. / Arteaga, C.L. / Sellers, W.R. / Ettenberg, S.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p59.cif.gz | 413.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p59.ent.gz | 337.8 KB | Display | PDB format |
PDBx/mmJSON format | 4p59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/4p59 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/4p59 | HTTPS FTP |
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-Related structure data
Related structure data | 1m6bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25480.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#3: Antibody | Mass: 23262.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Protein / Non-polymers , 2 types, 4 molecules A
#1: Protein | Mass: 69164.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: P21860, receptor protein-tyrosine kinase |
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#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 5 molecules
#4: Polysaccharide | #5: Sugar | |
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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: 3.5 Å3/Da / Density % sol: 64.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM bis-tris pH 6.5, 16% (w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→111.03 Å / Num. all: 22112 / Num. obs: 22112 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 74.13 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Rsym value: 0.118 / Net I/av σ(I): 6.714 / Net I/σ(I): 14.6 / Num. measured all: 148197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M6B Resolution: 3.4→111.03 Å / Cor.coef. Fo:Fc: 0.8891 / Cor.coef. Fo:Fc free: 0.8422 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.494
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Displacement parameters | Biso max: 246.71 Å2 / Biso mean: 97.29 Å2 / Biso min: 32.14 Å2
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Refinement step | Cycle: final / Resolution: 3.4→111.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.57 Å / Total num. of bins used: 11
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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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