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Yorodumi- PDB-3h3b: Crystal structure of the single-chain Fv (scFv) fragment of an an... -
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-Basic information
Entry | Database: PDB / ID: 3h3b | ||||||
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Title | Crystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21 in complex with residues 1-192 of ErbB2 extracellular domain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / beta-helix / protein-protein complex / ATP-binding / Disulfide bond / Kinase / Nucleotide-binding / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / PLCG1 events in ERBB2 signaling / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / semaphorin receptor complex ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / PLCG1 events in ERBB2 signaling / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / ERBB2 Regulates Cell Motility / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / PI3K events in ERBB2 signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of Rho protein signal transduction / neuromuscular junction development / 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 / ERBB2-ERBB3 signaling pathway / positive regulation of transcription by RNA polymerase I / oligodendrocyte differentiation / semaphorin-plexin signaling pathway / cellular response to epidermal growth factor stimulus / Signaling by ERBB2 / positive regulation of cell adhesion / positive regulation of protein targeting to membrane / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / regulation of angiogenesis / neurogenesis / SHC1 events in ERBB2 signaling / coreceptor activity / regulation of ERK1 and ERK2 cascade / Schwann cell development / basal plasma membrane / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / myelination / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of translation / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / ruffle membrane / wound healing / neuromuscular junction / peptidyl-tyrosine phosphorylation / neuron differentiation / transmembrane signaling receptor activity / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / heart development / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / receptor complex / positive regulation of MAPK cascade / cell surface receptor signaling pathway / endosome membrane / early endosome / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / protein heterodimerization activity / protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Zhou, H. / Liu, Y. / Niu, L. / Zhu, J. / Teng, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Insights into the Down-regulation of Overexpressed p185her2/neu Protein of Transformed Cells by the Antibody chA21. Authors: Zhou, H. / Zha, Z. / Liu, Y. / Zhang, H. / Zhu, J. / Hu, S. / Shen, G. / Cheng, L. / Niu, L. / Greene, M.I. / Teng, M. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h3b.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h3b.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 3h3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h3b_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 3h3b_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 3h3b_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 3h3b_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3b ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21669.643 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 23-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B References: UniProt: P04626, receptor protein-tyrosine kinase #2: Antibody | Mass: 27559.383 Da / Num. of mol.: 2 / Fragment: the single-chain Fv (scFv) fragment Source method: isolated from a genetically manipulated source Details: the scFv is derivated from A21 mAb(GeneBank Accession No. AY077780 for VH and AY077782 for VL), and constructed in VL-(Gly4Ser)4-VH mode. Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Gene: scFv of murine antibody A21 / Plasmid: pEE14 / Cell line (production host): CHO CELLS / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster) #3: Water | ChemComp-HOH / | Sequence details | REGARDING CHAIN B, THIS CONSISTS OF THREE PART. N- AND C- TERMINAL REGION CAN BE REFERRED TO ...REGARDING CHAIN B, THIS CONSISTS OF THREE PART. N- AND C- TERMINAL REGION CAN BE REFERRED TO AY077782 AND AY077780 IN GENBANK, RESPECTIVE | |
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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: 1.97 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% polyethylene glycol 4000, 100mM 3-(1-pyridino)-1-propane sulfonate, 100mM Na cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→29.91 Å / Num. obs: 29113 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4139 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 2GJJ and 2A91 Resolution: 2.45→29.91 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 18.834 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 2.064 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Total num. of bins used: 20
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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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