[English] 日本語
Yorodumi- PDB-4leo: Crystal structure of anti-HER3 Fab RG7116 in complex with the ext... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4leo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-HER3 Fab RG7116 in complex with the extracellular domains of human Her3 (ERBB3) | |||||||||
Components |
| |||||||||
Keywords | Transferase/Immune System / Fab fragment / Therapeutic antibody / Her3 receptor / Transferase-Immune System complex | |||||||||
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 / growth factor binding / protein tyrosine kinase activator activity / ERBB2-ERBB3 signaling pathway / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / negative regulation of signal transduction / Schwann cell development / extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 / myelination / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / SHC1 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / basal plasma membrane / Signaling by ERBB2 TMD/JMD mutants / wound healing / receptor protein-tyrosine kinase / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / heart development / regulation of cell population proliferation / 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 heterodimerization activity / apical plasma membrane / 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 | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | |||||||||
Authors | Schiller, C.B. / Hopfner, K.P. | |||||||||
Citation | Journal: Cancer Res. / Year: 2013 Title: RG7116, a Therapeutic Antibody That Binds the Inactive HER3 Receptor and Is Optimized for Immune Effector Activation. Authors: Mirschberger, C. / Schiller, C.B. / Schraml, M. / Dimoudis, N. / Friess, T. / Gerdes, C.A. / Reiff, U. / Lifke, V. / Hoelzlwimmer, G. / Kolm, I. / Hopfner, K.P. / Niederfellner, G. / Bossenmaier, B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4leo.cif.gz | 405.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4leo.ent.gz | 339.4 KB | Display | PDB format |
PDBx/mmJSON format | 4leo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4leo_validation.pdf.gz | 775.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4leo_full_validation.pdf.gz | 785.9 KB | Display | |
Data in XML | 4leo_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 4leo_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4leo ftp://data.pdbj.org/pub/pdb/validation_reports/le/4leo | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 24369.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
---|---|
#2: Antibody | Mass: 24231.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
-Protein / Non-polymers , 2 types, 151 molecules C
#3: Protein | Mass: 68378.500 Da / Num. of mol.: 1 / Fragment: UNP residues 20-631 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P21860, receptor protein-tyrosine kinase |
---|---|
#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 6 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350 , pH pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2012 |
Radiation | Monochromator: Horizontally side diffracting Silicon 111 crystal. Fixed wavelength (0.873) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→48.83 Å / Num. all: 35804 / Num. obs: 34229 / % possible obs: 95.6 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.64→2.8 Å / % possible all: 93.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→48.83 Å / SU ML: 0.36 / σ(F): 2 / Phase error: 27.82 / Stereochemistry target values: ML Details: SEVERAL ATOMS IN NAG C702 HAS BEEN SET TO ZERO OCCUPANCY BY PURPOSE, SINCE THEY ARE NOT COVERED BY THE 2FO-FC DENSITY AT 1.0 ANG SIGMA CONTOUR LEVEL
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→48.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 19.7348 Å / Origin y: 8.495 Å / Origin z: -20.5218 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |