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- PDB-7mxi: IgE-Fc in complex with DARPins E2_79 and E3_53 -

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Basic information

Entry
Database: PDB / ID: 7mxi
TitleIgE-Fc in complex with DARPins E2_79 and E3_53
Components
  • Anti-IgE Inhibitor E2_79
  • DARPin E3_53
  • IgE Fc
KeywordsIMMUNE SYSTEM / IgE / DARPin / Allergy / Inhibitor
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / FCERI mediated MAPK activation / antigen binding / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / inflammatory response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Ankyrin repeats (many copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Anti-ige inhibitor e2_79 / Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPennington, L.F. / Jardetzky, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115469 United States
CitationJournal: J.Allergy Clin.Immunol. / Year: 2021
Title: Structure-guided design of ultrapotent disruptive IgE inhibitors to rapidly terminate acute allergic reactions.
Authors: Pennington, L.F. / Gasser, P. / Brigger, D. / Guntern, P. / Eggel, A. / Jardetzky, T.S.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgE Fc
B: IgE Fc
C: DARPin E3_53
E: Anti-IgE Inhibitor E2_79
D: DARPin E3_53
F: Anti-IgE Inhibitor E2_79
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4559
Polymers123,7126
Non-polymers1,7443
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.908, 137.793, 88.250
Angle α, β, γ (deg.)90.000, 105.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IgE Fc / Immunoglobulin heavy constant epsilon / Ig epsilon chain C region / Ig epsilon chain C region ND


Mass: 27550.873 Da / Num. of mol.: 2 / Fragment: C3-4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Homo sapiens (human) / References: UniProt: P01854
#2: Protein DARPin E3_53


Mass: 18779.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein Anti-IgE Inhibitor E2_79


Mass: 15525.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: L7MTK7
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: E3_53, E2_79, and IgE-Fc3-4 were mixed in equimolar ratios with E3_53 and E2_79, and intact complexes were purified by SEC in 20 mM Tris-HCl, pH 8.0, 50mM NaCl and concentrated to 7mg/ml and ...Details: E3_53, E2_79, and IgE-Fc3-4 were mixed in equimolar ratios with E3_53 and E2_79, and intact complexes were purified by SEC in 20 mM Tris-HCl, pH 8.0, 50mM NaCl and concentrated to 7mg/ml and mixed 1:1 with acetate buffer pH 4.6, 43% ethylene glycol w/v in hanging drops

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→38.74 Å / Num. obs: 29053 / % possible obs: 98.65 % / Redundancy: 3.7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.1948 / Net I/σ(I): 5.07
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.8242 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 2901 / CC1/2: 0.577 / % possible all: 98.37

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gt7, 4grg, 4ycw

4gt7

4grg

4ycw


Resolution: 2.8→38.74 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 1278 4.4 %
Rwork0.2134 27772 -
obs0.2152 29050 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.01 Å2 / Biso mean: 61.1866 Å2 / Biso min: 18.63 Å2
Refinement stepCycle: final / Resolution: 2.8→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 116 0 7487
Biso mean--101.45 --
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067636
X-RAY DIFFRACTIONf_angle_d0.99810410
X-RAY DIFFRACTIONf_dihedral_angle_d11.1621090
X-RAY DIFFRACTIONf_chiral_restr0.0671231
X-RAY DIFFRACTIONf_plane_restr0.0081357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.910.33011470.27553078322599
2.91-3.040.3071430.25643108325199
3.04-3.210.29741440.25023074321899
3.21-3.410.26661380.23293071320999
3.41-3.670.27881390.23393049318898
3.67-4.040.26531460.21073084323099
4.04-4.620.23211410.19223089323099
4.62-5.820.22821390.19843091323098
5.82-38.740.2291410.18733128326999

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