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- PDB-5k33: Crystal structure of extracellular domain of HER2 in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k33 | |||||||||
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Title | Crystal structure of extracellular domain of HER2 in complex with Fcab STAB19 | |||||||||
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![]() | IMMUNE SYSTEM / antibody engineering / immunoglobulin G1 / Fc fragment / glycosylations / CH3 domain / Fcab / human epidermal growth factor receptor 2 / HER2/neu / erbB-2 / cell surface receptor | |||||||||
Function / homology | ![]() negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / Fc-gamma receptor I complex binding / regulation of microtubule-based process / ErbB-3 class receptor binding / complement-dependent cytotoxicity ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / Fc-gamma receptor I complex binding / regulation of microtubule-based process / ErbB-3 class receptor binding / complement-dependent cytotoxicity / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / IgG immunoglobulin complex / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / antibody-dependent cellular cytotoxicity / PLCG1 events in ERBB2 signaling / Classical antibody-mediated complement activation / neuromuscular junction development / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / positive regulation of Rho protein signal transduction / Initial triggering of complement / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / FCGR activation / positive regulation of protein targeting to membrane / Role of phospholipids in phagocytosis / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / immunoglobulin complex, circulating / cellular response to epidermal growth factor stimulus / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / GRB2 events in ERBB2 signaling / myelination / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Downregulation of ERBB2:ERBB3 signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / FCGR3A-mediated IL10 synthesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of epithelial cell proliferation / positive regulation of translation / FCGR3A-mediated phagocytosis / antigen binding / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / antibacterial humoral response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / positive regulation of MAPK cascade Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Humm, A. / Lobner, E. / Goritzer, K. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies. Authors: Lobner, E. / Humm, A.S. / Goritzer, K. / Mlynek, G. / Puchinger, M.G. / Hasenhindl, C. / Ruker, F. / Traxlmayr, M.W. / Djinovic-Carugo, K. / Obinger, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 454.9 KB | Display | ![]() |
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PDB format | ![]() | 382.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jihSC ![]() 5jiiC ![]() 5jikC ![]() 5kwgC ![]() 1n8zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 25567.920 Da / Num. of mol.: 1 Mutation: L358Y;T359L;K360S;N361D;Q362S;D413P;K414R;S415H; Q418A;Q418H 5 insertion at position 415a to 415e: SETMR Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 66989.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04626, receptor protein-tyrosine kinase |
-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/GOL.gif)
#5: Chemical | ChemComp-GOL / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.05 M MES, 10% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 27, 2015 / Details: CRL |
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→47.034 Å / Num. obs: 18446 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 112.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1422 / Net I/σ(I): 9.99 |
Reflection shell | Resolution: 3.3→3.418 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.652 / Mean I/σ(I) obs: 1.06 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JIH, 1N8Z Resolution: 3.3→47.034 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→47.034 Å
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Refine LS restraints |
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LS refinement shell |
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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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