[English] 日本語
Yorodumi- PDB-7ued: Crystal structure of full length mesothelin bound with MORAb-009 Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ued | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of full length mesothelin bound with MORAb-009 Fab | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Mesothelin | ||||||
Function / homology | Function and homology information Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region ...Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhan, J. / Esser, L. / Lin, D. / Tang, W.K. / Xia, D. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Cancer Res Commun / Year: 2023 Title: Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies. Authors: Zhan, J. / Lin, D. / Watson, N. / Esser, L. / Tang, W.K. / Zhang, A. / Liu, X. / Hassan, R. / Gleinich, A. / Shajahan, A. / Azadi, P. / Pastan, I. / Xia, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ued.cif.gz | 497.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ued.ent.gz | 345.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ued.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/7ued ftp://data.pdbj.org/pub/pdb/validation_reports/ue/7ued | HTTPS FTP |
---|
-Related structure data
Related structure data | 7u9jC 8cx3C 4f3fS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23140.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
---|---|
#3: Antibody | Mass: 23246.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
-Protein / Sugars , 2 types, 2 molecules M
#1: Protein | Mass: 35261.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13421 |
---|---|
#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 |
-Non-polymers , 3 types, 36 molecules
#5: Chemical | ChemComp-GOL / | ||
---|---|---|---|
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.81 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Tris, pH 7, 150 mM sodium citrate, 16.4% PEG3350, 100 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 21609 / % possible obs: 85 % / Redundancy: 3.1 % / Biso Wilson estimate: 66.66 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.444 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 1755 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F3F Resolution: 3→24.68 Å / SU ML: 0.3659 / Cross valid method: FREE R-VALUE / σ(F): 0.53 / Phase error: 22.7411 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→24.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|