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- PDB-8db4: Crystal structure of the peanut allergen Ara h 2 bound by two neu... -

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Basic information

Entry
Database: PDB / ID: 8db4
TitleCrystal structure of the peanut allergen Ara h 2 bound by two neutralizing antibodies 22S1 and 13T1
Components
  • 13T1 Heavy chain
  • 13T1 Light chain
  • 22S1 Heavy chain
  • 22S1 Light chain
  • Ara h 2 allergen
KeywordsALLERGEN/IMMUNE SYSTEM / Antibody / immunotherapy / immunoglobulin / ALLERGEN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


nutrient reservoir activity / metal ion binding
Similarity search - Function
Napin/ 2S seed storage protein/Conglutin / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich ...Napin/ 2S seed storage protein/Conglutin / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMin, J. / Pedersen, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES102906 United States
CitationJournal: 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
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 13T1 Heavy chain
B: 13T1 Light chain
C: 22S1 Heavy chain
D: 22S1 Light chain
E: Ara h 2 allergen
F: Ara h 2 allergen
G: 13T1 Heavy chain
H: 13T1 Light chain
I: 22S1 Heavy chain
J: 22S1 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,64520
Polymers222,99410
Non-polymers65110
Water5,531307
1
A: 13T1 Heavy chain
B: 13T1 Light chain
C: 22S1 Heavy chain
D: 22S1 Light chain
E: Ara h 2 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,88611
Polymers111,4975
Non-polymers3896
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Ara h 2 allergen
G: 13T1 Heavy chain
H: 13T1 Light chain
I: 22S1 Heavy chain
J: 22S1 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7599
Polymers111,4975
Non-polymers2624
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.796, 92.177, 96.180
Angle α, β, γ (deg.)95.040, 106.030, 108.870
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules EF

#5: Protein Ara h 2 allergen


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

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Antibody , 4 types, 8 molecules AGBHCIDJ

#1: Antibody 13T1 Heavy chain


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 13T1 Light chain


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 22S1 Heavy chain


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 22S1 Light chain


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)

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Non-polymers , 3 types, 317 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.05 M zinc acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LLY & 3OB4

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
RfactorNum. reflection% reflection
Rfree0.2461 2731 2.83 %
Rwork0.2111 93738 -
obs0.2121 96469 90.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14089 0 13 307 14409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003614474
X-RAY DIFFRACTIONf_angle_d0.675119733
X-RAY DIFFRACTIONf_chiral_restr0.04532248
X-RAY DIFFRACTIONf_plane_restr0.00442562
X-RAY DIFFRACTIONf_dihedral_angle_d12.94855073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.37211110.33944015X-RAY DIFFRACTION78.08
2.34-2.390.41571370.32874811X-RAY DIFFRACTION92.35
2.39-2.430.36741420.30654793X-RAY DIFFRACTION92.96
2.43-2.480.35271480.27694780X-RAY DIFFRACTION92.16
2.48-2.540.32451260.27134742X-RAY DIFFRACTION91.3
2.54-2.60.34411460.25564702X-RAY DIFFRACTION90.91
2.6-2.660.3091300.2644653X-RAY DIFFRACTION89.84
2.66-2.730.31691310.25374539X-RAY DIFFRACTION87.65
2.73-2.810.31351270.25024314X-RAY DIFFRACTION83.54
2.81-2.90.26351260.25063967X-RAY DIFFRACTION76.45
2.9-3.010.2841510.24084853X-RAY DIFFRACTION95.08
3.01-3.130.29241530.23974997X-RAY DIFFRACTION96.1
3.13-3.270.27881390.22564979X-RAY DIFFRACTION96.06
3.27-3.440.24711330.21954985X-RAY DIFFRACTION95.82
3.44-3.660.25591420.21434901X-RAY DIFFRACTION94.74
3.66-3.940.26381440.19664824X-RAY DIFFRACTION93.35
3.94-4.340.20351420.1794850X-RAY DIFFRACTION93.4
4.34-4.960.16521340.15524578X-RAY DIFFRACTION88.79
4.96-6.250.18371220.17624337X-RAY DIFFRACTION83.61
6.25-40.750.19381470.18035118X-RAY DIFFRACTION98.78

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