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- PDB-6oy4: Crystal structure of complex between recombinant Der p 2.0103 and... -

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Basic information

Entry
Database: PDB / ID: 6oy4
TitleCrystal structure of complex between recombinant Der p 2.0103 and Fab fragment of 7A1
Components
  • Der p 2 variant 3
  • Fab fragment of IgG, HEAVY CHAIN
  • Fab fragment of IgG, LIGHT CHAIN
Keywordsallergen/immune system / Allergen / dust mite / antibody binding / allergen-immune system complex
Function / homology
Function and homology information


sterol binding / sterol transport / extracellular region
Similarity search - Function
Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Der p 2 variant 3 / Mite group 2 allergen Der p 2
Similarity search - Component
Biological speciesDermatophagoides pteronyssinus (European house dust mite)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKapingidza, A.B. / Offermann, L.R. / Glesner, J. / Wunschmann, S. / Vailes, L.D. / Chapman, M.D.C. / Pomes, A. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI077653 United States
CitationJournal: J Immunol. / Year: 2019
Title: A Human IgE Antibody Binding Site on Der p 2 for the Design of a Recombinant Allergen for Immunotherapy.
Authors: Glesner, J. / Kapingidza, A.B. / Godzwon, M. / Offermann, L.R. / Mueller, G.A. / DeRose, E.F. / Wright, P. / Richardson, C.M. / Woodfolk, J.A. / Vailes, L.D. / Wunschmann, S. / London, R.E. ...Authors: Glesner, J. / Kapingidza, A.B. / Godzwon, M. / Offermann, L.R. / Mueller, G.A. / DeRose, E.F. / Wright, P. / Richardson, C.M. / Woodfolk, J.A. / Vailes, L.D. / Wunschmann, S. / London, R.E. / Chapman, M.D. / Ohlin, M. / Chruszcz, M. / Pomes, A.
History
DepositionMay 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 4, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Der p 2 variant 3
C: Fab fragment of IgG, LIGHT CHAIN
D: Fab fragment of IgG, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7194
Polymers61,6233
Non-polymers961
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-43 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.094, 43.336, 105.935
Angle α, β, γ (deg.)90.00, 125.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Der p 2 variant 3


Mass: 14141.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Production host: Komagataella pastoris (fungus) / References: UniProt: I2CMD6, UniProt: P49278*PLUS
#2: Antibody Fab fragment of IgG, LIGHT CHAIN


Mass: 23566.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 7A1-H1-G3 / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment of IgG, HEAVY CHAIN


Mass: 23914.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 7A1-H1-G3 / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM ammonium acetate, 30-55% 2-methyl-2,4-pentanediol at pH 6.5 (well solution)

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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: RAYONIX MX300-HS / Detector: CCD / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 23826 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.074 / Rrim(I) all: 0.133 / Rsym value: 0.114 / Net I/σ(I): 14.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1143 / CC1/2: 0.628 / Rpim(I) all: 0.325 / Rrim(I) all: 0.547 / Rsym value: 0.528 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KTJ, 3RVT

1ktj

3rvt


Resolution: 2.45→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.292 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26003 1142 4.8 %RANDOM
Rwork0.20305 ---
obs0.20583 22564 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.886 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0 Å2-0.79 Å2
2--3.61 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 5 221 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024301
X-RAY DIFFRACTIONr_bond_other_d00.023788
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9425859
X-RAY DIFFRACTIONr_angle_other_deg3.90438851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2125.263171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9161510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214772
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02818
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2543.0452213
X-RAY DIFFRACTIONr_mcbond_other1.2543.0442212
X-RAY DIFFRACTIONr_mcangle_it2.274.5482754
X-RAY DIFFRACTIONr_mcangle_other2.274.5482755
X-RAY DIFFRACTIONr_scbond_it0.9723.0162088
X-RAY DIFFRACTIONr_scbond_other0.9693.0082085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.694.4843099
X-RAY DIFFRACTIONr_long_range_B_refined4.50933.3184391
X-RAY DIFFRACTIONr_long_range_B_other4.41933.2114369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 95 -
Rwork0.257 1568 -
obs--90.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.58070.58050.64051.9647-0.56912.61210.0418-0.6506-0.71340.27010.0425-0.09090.0673-0.0114-0.08430.07010.06660.03660.3510.24370.24849.327-45.54917.386
20.62160.26940.2570.2655-0.03761.2811-0.11690.0903-0.0567-0.02580.03680.001-0.23340.12070.08010.1348-0.01910.00890.038-0.00010.028943.129-19.917-14.829
31.09680.4407-0.5880.3089-0.08341.5092-0.0380.1848-0.1357-0.02520.0187-0.0193-0.1992-0.22660.01940.08920.04530.01270.087-0.03830.036626.33-22.93-21.912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 129
2X-RAY DIFFRACTION2C1 - 216
3X-RAY DIFFRACTION3D1 - 221

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