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- PDB-6uqr: Complex of IgE and Ligelizumab -

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Basic information

Entry
Database: PDB / ID: 6uqr
TitleComplex of IgE and Ligelizumab
Components
  • IgE
  • Ligelizumab
KeywordsIMMUNE SYSTEM / anti-IgE antibody / complex / monoclonal
Function / homology
Function and homology information


IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / 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 ...IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / 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
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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 3.65029109708 Å
AuthorsTarchevskaya, S.S. / Kleinboelting, S. / Jardetzky, T.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI115469 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL141493 United States
CitationJournal: Nat Commun / Year: 2020
Title: The mechanistic and functional profile of the therapeutic anti-IgE antibody ligelizumab differs from omalizumab.
Authors: Gasser, P. / Tarchevskaya, S.S. / Guntern, P. / Brigger, D. / Ruppli, R. / Zbaren, N. / Kleinboelting, S. / Heusser, C. / Jardetzky, T.S. / Eggel, A.
History
DepositionOct 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ligelizumab
B: IgE
C: Ligelizumab
D: IgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6936
Polymers113,0334
Non-polymers1,6602
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.960, 103.180, 124.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNTHRTHR(chain 'A' and (resid 1 through 37 or (resid 38...AA1 - 1171 - 117
121GLUGLUVALVAL(chain 'A' and (resid 1 through 37 or (resid 38...AA144 - 247144 - 247
211GLNGLNTHRTHR(chain 'C' and (resid 1 through 98 or (resid 99...CC1 - 1171 - 117
221GLUGLUVALVAL(chain 'C' and (resid 1 through 98 or (resid 99...CC144 - 247144 - 247
112ARGARGPROPRO(chain 'B' and ((resid 334 and (name N or name...BB334 - 54536 - 247
212ARGARGPROPRO(chain 'D' and (resid 334 through 379 or (resid 380...DD334 - 54536 - 247

NCS ensembles :
ID
1
2

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Components

#1: Antibody Ligelizumab


Mass: 28965.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: anti-IgE antibody / Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293-6E / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Protein IgE / 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 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: P01854
#3: 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.: 1
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
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.2M Na Thiocyanate pH 6.9, 20% PEG3350, 10 mM Spermidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.65→47.9 Å / Num. obs: 11282 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 112.188066571 Å2 / CC1/2: 1 / Rrim(I) all: 0.33 / Net I/σ(I): 8.4
Reflection shellResolution: 3.65→3.7 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 430 / CC1/2: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y7Q, 4F9P

2y7q

4f9p


Resolution: 3.65029109708→19.954204639 Å / SU ML: 0.710454924916 / Cross valid method: FREE R-VALUE / σ(F): 1.35615677935 / Phase error: 35.3580034178
RfactorNum. reflection% reflection
Rfree0.295281674461 558 5.00807754443 %
Rwork0.290414730496 --
obs0.290662214839 11142 99.9372140999 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 113.182185354 Å2
Refinement stepCycle: LAST / Resolution: 3.65029109708→19.954204639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 111 0 6822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004874243433147025
X-RAY DIFFRACTIONf_angle_d0.9358700610699605
X-RAY DIFFRACTIONf_chiral_restr0.05030785559061077
X-RAY DIFFRACTIONf_plane_restr0.006104737042971217
X-RAY DIFFRACTIONf_dihedral_angle_d14.16703108994136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6503-4.01490.4159052261991370.3821853592412595X-RAY DIFFRACTION99.8538011696
4.0149-4.58970.3111853920371370.3193557051922603X-RAY DIFFRACTION100
4.5897-5.75940.2922923632071390.2853156467822648X-RAY DIFFRACTION99.9641319943
5.7594-19.95420.2510701404641450.2499193007272738X-RAY DIFFRACTION99.9306759099
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)
13.956966369290.958637310531.756930604773.79370337273-3.088838262214.004920623270.4644143699350.2304040211920.2769268849760.01226943232650.1534447406140.7161730835380.655489123320.108632183332-0.4006557906121.110863822770.2955864386230.1224612066760.5454842629390.0656951200571.2132131690923.169762429182.99494986672.07105629717
26.34357053293-0.428946830125-1.044106023982.24305131422.75758502628.071099860080.0600237243365-0.1091144239730.6364891162350.248731427621-0.149886284007-0.03883114567190.7231112788870.62399596264-0.4082688496980.38613715214-0.0216466227796-0.06986830637330.8137625221720.3561342928611.213279258737.5793116146107.2322792018.80685277855
37.560157939751.78218520283-0.6614981324274.17110587149-0.1917807932413.10445017523-0.7732983791370.3102778396910.325750795021-0.7611665052670.1913025531630.263214736416-0.0744788246216-1.091800747890.2179585229111.088744810020.0654449096864-0.382145699260.800385679987-0.03615059660081.24942975845-1.1143970047113.32999537214.0894021871
42.66358407334-1.92621190126-1.246193572.795892936432.230373039623.810816424380.8433726952040.01888679837010.627826832697-0.4121756210780.119242254009-1.36940813793-0.5093944422050.451277717876-0.4841444748810.9197361071-0.2017931431710.06852672366870.6730257225580.2249036509461.7258628527626.3254171184121.7377702868.47385104981
51.712854857950.2956463126850.2397511037182.093356630121.140717335454.15329370568-0.0347982269508-0.1069198142030.0965641635744-0.06671132874650.01475138440180.600575683510.690661421518-0.5117007277060.08331331449220.766260290346-0.1217261433090.1701362102630.658734175910.0571563010541.217720117256.3210505141583.7228888851-20.9033485804
64.66977836973-0.0600292903175-1.995961783912.289734906380.738872066863.046579431520.152920446844-0.841390749508-0.611809924213-0.242706033498-0.4632483056840.1985402069230.404165822845-1.260730642860.1015259742580.755032489519-0.293577807349-0.2448229483361.505526161330.01997047591311.11695354608-4.2772021770597.133941473136.0687917867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 334 through 439)
2X-RAY DIFFRACTION2chain 'B' and (resid 440 through 545)
3X-RAY DIFFRACTION3chain 'D' and (resid 334 through 439)
4X-RAY DIFFRACTION4chain 'D' and (resid 440 through 545)
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 247)
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 247)

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