[English] 日本語
Yorodumi- PDB-8db4: Crystal structure of the peanut allergen Ara h 2 bound by two neu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8db4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the peanut allergen Ara h 2 bound by two neutralizing antibodies 22S1 and 13T1 | ||||||
Components |
| ||||||
Keywords | ALLERGEN/IMMUNE SYSTEM / Antibody / immunotherapy / immunoglobulin / ALLERGEN-IMMUNE SYSTEM complex | ||||||
Function / homology | Napin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / Ara h 2 allergen Function and homology information | ||||||
Biological species | Homo sapiens (human) Arachis hypogaea (peanut) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Min, J. / Pedersen, L.C. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Clin.Invest. / Year: 2023 Title: Immunotherapy-induced neutralizing antibodies disrupt allergen binding and sustain allergen tolerance in peanut allergy. Authors: LaHood, N.A. / Min, J. / Keswani, T. / Richardson, C.M. / Amoako, K. / Zhou, J. / Marini-Rapoport, O. / Bernard, H. / Hazebrouck, S. / Shreffler, W.G. / Love, J.C. / Pomes, A. / Pedersen, L. ...Authors: LaHood, N.A. / Min, J. / Keswani, T. / Richardson, C.M. / Amoako, K. / Zhou, J. / Marini-Rapoport, O. / Bernard, H. / Hazebrouck, S. / Shreffler, W.G. / Love, J.C. / Pomes, A. / Pedersen, L.C. / Mueller, G.A. / Patil, S.U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8db4.cif.gz | 408.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8db4.ent.gz | 297.4 KB | Display | PDB format |
PDBx/mmJSON format | 8db4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/8db4 ftp://data.pdbj.org/pub/pdb/validation_reports/db/8db4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ob4S 4llyS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules EF
#5: Protein | Mass: 15660.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arachis hypogaea (peanut) / Gene: Ara h 2, Ahy_A08g040012 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A445BYI5 |
---|
-Antibody , 4 types, 8 molecules AGBHCIDJ
#1: Antibody | Mass: 24478.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 23665.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 24291.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #4: Antibody | Mass: 23401.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
---|
-Non-polymers , 3 types, 317 molecules
#6: Chemical | ChemComp-ZN / #7: Chemical | ChemComp-EDO / | #8: 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: 2.79 Å3/Da / Density % sol: 55.98 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.05 M zinc acetate, 20% PEG3350 |
-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: Apr 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 96622 / % possible obs: 91.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 42.32 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.091 / Χ2: 1.154 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4898 / CC1/2: 0.795 / CC star: 0.941 / Rpim(I) all: 0.463 / Rrim(I) all: 0.902 / Χ2: 0.492 / % possible all: 93.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4LLY & 3OB4 Resolution: 2.3→40.75 Å / SU ML: 0.3383 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.1763 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: 54.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|