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- PDB-3h9y: Crystal structure of the IgE-Fc3-4 domains -

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Basic information

Entry
Database: PDB / ID: 3h9y
TitleCrystal structure of the IgE-Fc3-4 domains
ComponentsIg epsilon chain C region
KeywordsIMMUNE SYSTEM / Immunoglobin / IgE / Fc / flexibility / hydrophobic pocket / Disulfide bond / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain
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 / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / immunoglobulin complex, circulating / B cell proliferation / immunoglobulin receptor binding / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / 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 / 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 / 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
AMMONIUM ION / Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsWurzburg, B.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Conformational flexibility in immunoglobulin E-Fc 3-4 revealed in multiple crystal forms.
Authors: Wurzburg, B.A. / Jardetzky, T.S.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3May 30, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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.label_asym_id / _atom_site.label_entity_id / _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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Ig epsilon chain C region
B: Ig epsilon chain C region
E: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6737
Polymers74,7603
Non-polymers2,9134
Water4,450247
1
A: Ig epsilon chain C region
hetero molecules

B: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8244
Polymers49,8402
Non-polymers1,9842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5530 Å2
ΔGint21 kcal/mol
Surface area22630 Å2
MethodPISA
2
E: Ig epsilon chain C region
hetero molecules

E: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6986
Polymers49,8402
Non-polymers1,8584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area5400 Å2
ΔGint27 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.676, 104.994, 49.222
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ig epsilon chain C region


Mass: 24920.146 Da / Num. of mol.: 3 / Fragment: UNP residues 209-428 / Mutation: N252Q, N264Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: P01854
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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.: 2
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: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by ...Details: 1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.00796 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 30, 1998
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00796 Å / Relative weight: 1
ReflectionResolution: 2.23→30 Å / Num. all: 36675 / Num. obs: 36675 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.061 / Net I/σ(I): 20.943
Reflection shellResolution: 2.23→2.38 Å / Redundancy: 3.45 % / Rsym value: 0.513 / % possible all: 89.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.94 Å
Translation2.5 Å28.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partially-refined monomer (chain C) from the IgE-Fc3-4 carbohydrate mutant P21 crystal form.

Resolution: 2.23→29.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.167 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26212 1866 5.1 %RANDOM
Rwork0.23101 ---
obs0.23263 36671 97.91 %-
all-36671 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.08 Å2
2--0.86 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.23→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 195 247 5410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225313
X-RAY DIFFRACTIONr_bond_other_d0.0010.023713
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.997259
X-RAY DIFFRACTIONr_angle_other_deg0.7523.0038929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.49922.267225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73715847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4321554
X-RAY DIFFRACTIONr_chiral_restr0.0670.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021060
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_it1.15323159
X-RAY DIFFRACTIONr_mcbond_other0.19921234
X-RAY DIFFRACTIONr_mcangle_it1.92835168
X-RAY DIFFRACTIONr_scbond_it1.04922154
X-RAY DIFFRACTIONr_scangle_it1.62132091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.35 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.447 234 -
Rwork0.36 4440 -
obs--86.48 %
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)
11.29570.39130.5864.6031-0.78073.28490.114-0.1669-0.02990.0545-0.12370.59140.1455-0.54250.0098-0.0233-0.0314-0.0218-0.1526-0.04380.014511.664649.46659.2828
210.9997-4.12955.55171.5503-2.08422.8020.11960.034-0.0522-0.0722-0.1396-0.0339-0.0410.08370.02010.0413-0.0219-0.010.00260.00620.012430.002950.014168.781
31.5837-0.21980.2892.6348-0.05182.18250.05950.29020.0967-0.0423-0.1015-0.17420.03720.05880.0419-0.1067-0.00480.018-0.03670.0242-0.068327.114725.564866.0729
42.77130.329-0.08043.4153-0.32562.5266-0.0202-0.0160.3799-0.0180.03980.2611-0.325-0.0607-0.0196-0.0784-0.01310.0225-0.0028-0.0419-0.12188.317335.498441.6861
52.7712-2.9049-3.58743.51734.78436.86340.0119-0.10660.0056-0.03810.0531-0.28630.04580.2847-0.065-0.0277-0.03450.02130.08330.0177-0.03149.730217.391533.3219
62.91360.0911-0.38081.10490.02581.6455-0.0237-0.03490.1570.1541-0.0054-0.1104-0.01130.00320.0291-0.0149-0.0165-0.0298-0.0897-0.0061-0.070834.419722.442134.2315
71.91180.2706-0.17771.87840.48542.33720.0905-0.2782-0.39350.3246-0.08150.18890.2210.027-0.0089-0.0566-0.07430.0128-0.1567-0.0125-0.012557.082237.217355.0462
89.6506-10.5621-10.715711.559711.727711.8982-1.0079-0.0673-0.06060.50320.11190.4518-0.0397-0.18740.8960.1066-0.04770.10670.0184-0.0502-0.013641.88449.472161.6624
92.7426-0.07650.14541.0899-0.12051.31590.02880.0791-0.05990.0145-0.05870.01790.00150.14850.0299-0.1050.01550.00440.0566-0.0079-0.119561.364564.119363.7129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION1A336 - 433
3X-RAY DIFFRACTION2A434 - 440
4X-RAY DIFFRACTION3A441 - 544
5X-RAY DIFFRACTION4B1 - 5
6X-RAY DIFFRACTION4B335 - 433
7X-RAY DIFFRACTION5B434 - 440
8X-RAY DIFFRACTION6B441 - 544
9X-RAY DIFFRACTION7E1 - 5
10X-RAY DIFFRACTION7E336 - 433
11X-RAY DIFFRACTION8E434 - 440
12X-RAY DIFFRACTION9E441 - 544

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