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- PDB-5hys: Structure of IgE complexed with omalizumab -

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Basic information

Entry
Database: PDB / ID: 5hys
TitleStructure of IgE complexed with omalizumab
Components
  • Epididymis luminal protein 214
  • Ig epsilon chain C region
  • Uncharacterized protein
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / type 2 immune response / immunoglobulin receptor binding / immunoglobulin complex, circulating / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / immune response / inflammatory response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPennington, L.F. / Tarchevskaya, S.S. / Sathiyamoorthy, K. / Jardetzky, T.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)PR130130 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI104209 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007290 United States
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of omalizumab therapy and omalizumab-mediated IgE exchange.
Authors: Pennington, L.F. / Tarchevskaya, S. / Brigger, D. / Sathiyamoorthy, K. / Graham, M.T. / Nadeau, K.C. / Eggel, A. / Jardetzky, T.S.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Epididymis luminal protein 214
L: Uncharacterized protein
A: Epididymis luminal protein 214
B: Uncharacterized protein
C: Epididymis luminal protein 214
D: Uncharacterized protein
E: Epididymis luminal protein 214
F: Uncharacterized protein
G: Ig epsilon chain C region
I: Ig epsilon chain C region
J: Ig epsilon chain C region
K: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,10864
Polymers292,85412
Non-polymers8,25452
Water1,06359
1
H: Epididymis luminal protein 214
L: Uncharacterized protein
A: Epididymis luminal protein 214
B: Uncharacterized protein
G: Ig epsilon chain C region
I: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,36230
Polymers146,4276
Non-polymers3,93524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Epididymis luminal protein 214
D: Uncharacterized protein
E: Epididymis luminal protein 214
F: Uncharacterized protein
J: Ig epsilon chain C region
K: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,74634
Polymers146,4276
Non-polymers4,31928
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.103, 107.143, 151.043
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules HACELBDF

#1: Antibody
Epididymis luminal protein 214


Mass: 23653.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEL-214 / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
Uncharacterized protein


Mass: 23922.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 8 molecules GIJK

#3: Protein
Ig epsilon chain C region


Mass: 25637.812 Da / Num. of mol.: 4 / Fragment: Ig-like 3 and Ig-like 4 domains, residues 209-428 / Mutation: C328A, G335C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01854
#4: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 107 molecules

#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium Sulfate, 0.1 M Tris pH 8.5, and 41% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2015 / Details: Rh coated
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→37.61 Å / Num. obs: 107558 / % possible obs: 97.8 % / Observed criterion σ(F): 1.94 / Observed criterion σ(I): -3 / Redundancy: 26.9 % / Biso Wilson estimate: 61.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1148 / Rsym value: 0.1169 / Net I/σ(I): 22.09
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 23 % / Rmerge(I) obs: 2.009 / Mean I/σ(I) obs: 1.94 / % possible all: 95.73

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20000.98.691hdata reduction
PHENIXv1.9phasing
HKL-20000.98.691hdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GT7 and 4X7S

4gt7

4x7s


Resolution: 2.5→37.607 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1512 1.41 %Random selection
Rwork0.221 ---
obs0.221 107541 97.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.6 Å2 / Biso mean: 71.0647 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.5→37.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20083 0 484 59 20626
Biso mean--99.05 61.09 -
Num. residues----2604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321132
X-RAY DIFFRACTIONf_angle_d0.81228784
X-RAY DIFFRACTIONf_chiral_restr0.033227
X-RAY DIFFRACTIONf_plane_restr0.0043631
X-RAY DIFFRACTIONf_dihedral_angle_d12.8237616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58070.32061330.34379348948195
2.5807-2.67290.34021380.31799679981799
2.6729-2.77990.33731390.30549659979899
2.7799-2.90640.32991370.29719641977898
2.9064-3.05950.33591370.29339608974598
3.0595-3.25110.28971350.26599500963597
3.2511-3.5020.28971390.24339710984999
3.502-3.85410.2611390.22149764990399
3.8541-4.4110.17651360.18179571970797
4.411-5.55450.17541400.16149798993899
5.5545-37.61090.20931390.1799751989097

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