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- PDB-5nqw: IgE-Fc in complex with single domain antibody 026 -

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Basic information

Entry
Database: PDB / ID: 5nqw
TitleIgE-Fc in complex with single domain antibody 026
Components
  • 026
  • Immunoglobulin heavy constant epsilon
KeywordsIMMUNE SYSTEM / IgE-Fc / nanobody / VHH / allergy
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 / immunoglobulin complex, circulating / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / antigen binding / FCERI mediated MAPK activation / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / inflammatory response / immune 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 / 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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLaursen, N.S. / Jabs, F. / Spillner, E. / Andersen, G.R.
CitationJournal: Nat Commun / Year: 2018
Title: Trapping IgE in a closed conformation by mimicking CD23 binding prevents and disrupts Fc epsilon RI interaction.
Authors: Jabs, F. / Plum, M. / Laursen, N.S. / Jensen, R.K. / Molgaard, B. / Miehe, M. / Mandolesi, M. / Rauber, M.M. / Pfutzner, W. / Jakob, T. / Mobs, C. / Andersen, G.R. / Spillner, E.
History
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy constant epsilon
B: Immunoglobulin heavy constant epsilon
C: 026
D: 026
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8298
Polymers77,1744
Non-polymers2,6544
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint32 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.020, 102.020, 300.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 23834.979 Da / Num. of mol.: 2
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: Antibody 026


Mass: 14752.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 5.06 Å3/Da / Density % sol: 75.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole pH 7.0 11-12 % polyethylene glycol 20.000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 22583 / % possible obs: 99 % / Redundancy: 12.3 % / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WQR

2wqr


Resolution: 3.4→19.993 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.38
RfactorNum. reflection% reflection
Rfree0.2409 2000 8.86 %
Rwork0.2123 --
obs0.2149 22561 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 178 0 5404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045552
X-RAY DIFFRACTIONf_angle_d4.7177614
X-RAY DIFFRACTIONf_dihedral_angle_d11.2193352
X-RAY DIFFRACTIONf_chiral_restr0.716881
X-RAY DIFFRACTIONf_plane_restr0.007957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.48470.40281370.37011401X-RAY DIFFRACTION100
3.4847-3.57840.35011390.31481432X-RAY DIFFRACTION100
3.5784-3.68310.36741410.33691447X-RAY DIFFRACTION100
3.6831-3.80120.33041410.29181459X-RAY DIFFRACTION100
3.8012-3.93610.31691390.29761434X-RAY DIFFRACTION100
3.9361-4.09240.27781420.24921452X-RAY DIFFRACTION100
4.0924-4.27690.23591400.21521446X-RAY DIFFRACTION100
4.2769-4.49990.20311410.19151451X-RAY DIFFRACTION100
4.4999-4.77830.21621420.16261459X-RAY DIFFRACTION100
4.7783-5.14140.17751450.16981475X-RAY DIFFRACTION100
5.1414-5.64820.24571440.16561482X-RAY DIFFRACTION100
5.6482-6.44150.21341440.19521491X-RAY DIFFRACTION100
6.4415-8.02720.20541490.19291528X-RAY DIFFRACTION100
8.0272-19.99350.21611560.19011604X-RAY DIFFRACTION100
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)
14.18020.23521.57411.5651-1.4584.27010.2893-0.3770.17260.5461-0.2829-0.098-0.81110.5875-0.040.9788-0.11640.05411.73310.03920.95562.1016-20.5394-24.3522
23.5012-0.3571-1.58032.0224-0.87073.31350.0580.0316-0.2924-0.5663-0.1279-0.09240.5220.7918-0.00010.9940.15870.00011.37250.03761.0855-3.3348-40.2155-43.9662
31.9842-1.02130.21483.8682-1.6924.02610.367-0.21820.2620.27240.09330.2795-0.57270.0289-0.04490.8029-0.06480.14041.26380.06761.2646-26.5423-11.2574-38.3244
43.02381.06750.43032.4849-2.28443.5981-0.0487-0.0972-0.5552-0.32580.2970.16020.6607-0.3283-0.00010.9746-0.0856-0.03461.07680.09571.1231-20.6741-36.729-49.2028
54.80651.6910.36185.3512-1.28073.25340.1533-0.34540.0199-0.0599-0.16570.2054-0.1926-0.0436-00.64370.07630.05810.95650.0790.8357-2.1927-9.7216-61.3531
63.7302-1.5603-0.47463.55070.26043.9374-0.1707-1.0509-0.38980.20370.101-0.00480.18030.457700.77990.02540.00661.44860.26231.0422-21.9115-41.9292-14.3223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 336:436 or resid 545)
2X-RAY DIFFRACTION2chain A and resid 437:545
3X-RAY DIFFRACTION3chain B and (resid 334:436 or resid 545)
4X-RAY DIFFRACTION4chain B and resid 437:544
5X-RAY DIFFRACTION5chain C
6X-RAY DIFFRACTION6chain D

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