+Open data
-Basic information
Entry | Database: PDB / ID: 1n8y | |||||||||
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Title | Crystal structure of the extracellular region of rat HER2 | |||||||||
Components | protooncoprotein | |||||||||
Keywords | TRANSFERASE / tyrosin kinase receptor / cell surface receptor | |||||||||
Function / homology | Function and homology information Signaling by ERBB2 / GRB7 events in ERBB2 signaling / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / GRB2 events in ERBB2 signaling / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse ...Signaling by ERBB2 / GRB7 events in ERBB2 signaling / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / GRB2 events in ERBB2 signaling / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / SHC1 events in ERBB2 signaling / PIP3 activates AKT signaling / negative regulation of immature T cell proliferation in thymus / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / mammary gland involution / immature T cell proliferation in thymus / RNA polymerase I core binding / lateral loop / glial cell differentiation / sympathetic nervous system development / peripheral nervous system development / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / positive regulation of Ras protein signal transduction / motor neuron axon guidance / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / tongue development / neuromuscular junction development / ERBB2-EGFR signaling pathway / positive regulation of Rho protein signal transduction / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / regulation of cell differentiation / microvillus / semaphorin-plexin signaling pathway / positive regulation of cell adhesion / estrous cycle / response to axon injury / positive regulation of protein targeting to membrane / coreceptor activity / Schwann cell development / skeletal muscle tissue development / cellular response to epidermal growth factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / myelination / transmembrane receptor protein tyrosine kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / liver development / positive regulation of epithelial cell proliferation / response to progesterone / positive regulation of translation / wound healing / Hsp90 protein binding / neuromuscular junction / neuron differentiation / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / ruffle membrane / transmembrane signaling receptor activity / myelin sheath / presynaptic membrane / nervous system development / heart development / regulation of cell population proliferation / cytoplasmic vesicle / positive regulation of cell growth / basolateral plasma membrane / postsynaptic membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / early endosome / receptor complex / endosome membrane / intracellular signal transduction / response to xenobiotic stimulus / positive regulation of protein phosphorylation / apical plasma membrane / protein heterodimerization activity / phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Cho, H.-S. / Mason, K. / Ramyar, K.X. / Stanley, A.M. / Gabelli, S.B. / Denney Jr., D.W. / Leahy, D.J. | |||||||||
Citation | Journal: Nature / Year: 2003 Title: Structure of the Extracellular Region of HER2 Alone and in complex with the Herceptin Fab Authors: Cho, H.-S. / Mason, K. / Ramyar, K.X. / Stanley, A.M. / Gabelli, S.B. / Denney Jr., D.W. / Leahy, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n8y.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n8y.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n8y_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1n8y_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1n8y_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 1n8y_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n8y ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n8y | HTTPS FTP |
-Related structure data
Related structure data | 1n8zC 1m6bS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 67361.422 Da / Num. of mol.: 1 / Fragment: extracellular region (residues 26-633) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: neu / Plasmid: pSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO(Lec1) / References: GenBank: 22651765, UniProt: P06494*PLUS | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.05 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 15-30% PEG4000, 50mM Na citrate pH5.4, 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 34177 / Num. obs: 33900 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.77 / % possible all: 93.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 34177 / Redundancy: 3.7 % / Num. measured all: 196228 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 93.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M6B Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.33 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.364 / ESU R Free: 0.28
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.924 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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