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- PDB-4ezm: Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B ... -

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Basic information

Entry
Database: PDB / ID: 4ezm
TitleCrystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23
Components
  • Ig epsilon chain C region
  • Low affinity immunoglobulin epsilon Fc receptor
KeywordsIMMUNE SYSTEM / Immunoglobulin fold Lectin / Antibody Receptor
Function / homology
Function and homology information


low-affinity IgE receptor activity / 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 / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / eosinophil degranulation ...low-affinity IgE receptor activity / 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 / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / IgE binding / type 2 immune response / positive regulation of killing of cells of another organism / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / immunoglobulin complex, circulating / B cell proliferation / immunoglobulin receptor binding / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / positive regulation of nitric-oxide synthase activity / FCERI mediated MAPK activation / B cell receptor signaling pathway / FCERI mediated NF-kB activation / integrin binding / antibacterial humoral response / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / immune response / inflammatory response / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Immunoglobulin heavy constant epsilon / Low affinity immunoglobulin epsilon Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDhaliwal, B. / Yuan, D. / Sutton, B.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of IgE bound to its B-cell receptor CD23 reveals a mechanism of reciprocal allosteric inhibition with high affinity receptor Fc{varepsilon}RI.
Authors: Dhaliwal, B. / Yuan, D. / Pang, M.O. / Henry, A.J. / Cain, K. / Oxbrow, A. / Fabiane, S.M. / Beavil, A.J. / McDonnell, J.M. / Gould, H.J. / Sutton, B.J.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.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.type_symbol / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig epsilon chain C region
B: Ig epsilon chain C region
C: Ig epsilon chain C region
D: Ig epsilon chain C region
E: Ig epsilon chain C region
F: Ig epsilon chain C region
G: Low affinity immunoglobulin epsilon Fc receptor
H: Low affinity immunoglobulin epsilon Fc receptor
I: Low affinity immunoglobulin epsilon Fc receptor
J: Low affinity immunoglobulin epsilon Fc receptor
K: Low affinity immunoglobulin epsilon Fc receptor
L: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,33620
Polymers246,51112
Non-polymers5,8258
Water181
1
A: Ig epsilon chain C region
B: Ig epsilon chain C region
G: Low affinity immunoglobulin epsilon Fc receptor
H: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9926
Polymers82,1704
Non-polymers1,8222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ig epsilon chain C region
D: Ig epsilon chain C region
I: Low affinity immunoglobulin epsilon Fc receptor
J: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3528
Polymers82,1704
Non-polymers2,1824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ig epsilon chain C region
F: Ig epsilon chain C region
K: Low affinity immunoglobulin epsilon Fc receptor
L: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9926
Polymers82,1704
Non-polymers1,8222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.890, 110.750, 376.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ig epsilon chain C region


Mass: 24920.146 Da / Num. of mol.: 6 / Fragment: Human IgE-Fc(epsilon)3-4, UNP residues 209-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Cell line (production host): HEK293 / Production host: Homo Sapiens (human) / References: UniProt: P01854
#2: Protein
Low affinity immunoglobulin epsilon Fc receptor / BLAST-2 / C-type lectin domain family 4 member J / Fc-epsilon-RII / Immunoglobulin E-binding factor ...BLAST-2 / C-type lectin domain family 4 member J / Fc-epsilon-RII / Immunoglobulin E-binding factor / Lymphocyte IgE receptor / Low affinity immunoglobulin epsilon Fc receptor membrane-bound form / Low affinity immunoglobulin epsilon Fc receptor soluble form


Mass: 16164.986 Da / Num. of mol.: 6 / Fragment: Human derCD23, UNP residues 156-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCER2, CD23A, CLEC4J, FCE2, IGEBF / Production host: Escherichia coli (E. coli) / References: UniProt: P06734
#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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→29.87 Å / Num. all: 48290 / Num. obs: 48290 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 117.08 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H9Z, 2H2R

3h9z

2h2r


Resolution: 3.1→29.87 Å / Cor.coef. Fo:Fc: 0.7819 / Cor.coef. Fo:Fc free: 0.7637 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 2437 5.05 %THIN SHELLS
Rwork0.264 ---
all0.2831 48290 --
obs0.2649 48290 --
Displacement parametersBiso mean: 110.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.6399 Å20 Å20 Å2
2--5.7564 Å20 Å2
3----4.1165 Å2
Refine analyzeLuzzati coordinate error obs: 0.799 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16104 0 388 1 16493
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.04116968HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2923059HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5726SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes373HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2437HARMONIC5
X-RAY DIFFRACTIONt_it16968HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion19.65
X-RAY DIFFRACTIONt_chiral_improper_torsion2257SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact17838SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2551 169 5 %
Rwork0.2525 3208 -
all0.2526 3377 -
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.3815-1.7518-1.47092.83330.32832.0708-0.0887-0.1314-0.2493-0.05780.1229-0.08120.18510.1044-0.0341-0.10050.00220.1069-0.061-0.01140.0845-3.5254-9.022790.8039
2refined3.59411.9686-1.56692.2903-0.69332.1256-0.29240.3869-0.4351-0.04770.1209-0.14030.226-0.30080.1715-0.0842-0.00740.1819-0.035-0.08660.0201-29.8883-5.281392.6918
3refined-16.1029-12.91830.3872
4refined3.0851-0.2125-0.97031.46710.43351.9108-0.0060.34050.0202-0.299-0.0831-0.1205-0.2424-0.05770.0891-0.1665-0.01030.14080.1012-0.18730.0511-30.01098.875933.1758
5refined3.810861.489431.1989
6refined2.12430.5826-0.36234.54322.30872.5346-0.0987-0.3691-0.00720.30820.42280.07320.23150.5775-0.324-0.16070.14570.08780.0674-0.3004-0.066415.086738.739228.9882
7refined4.7734-0.6134-0.95152.0533-0.54314.6686-0.0510.3032-0.1429-0.1465-0.0066-0.05680.66370.31730.05770.01790.15930.2082-0.0297-0.1542-0.009915.1607-11.855760.1829
8refined6.47680.9792-2.6583.0045-0.34833.29260.1619-0.3892-0.31610.6339-0.25160.23710.08480.11050.08970.1718-0.13230.316-0.17710.134-0.0289-48.2666-10.8271123.364
9refined0.9629-0.4704-0.19336.20083.49172.99810.02630.3377-0.1974-0.552-0.1474-0.007-0.0176-0.21350.12110.2807-0.27230.1671-0.0034-0.456-0.2221-13.8601-32.98330.4169
10refined6.215-1.9257-1.60084.7577-0.12552.40220.184-0.35080.0570.2181-0.02660.1556-0.33840.1105-0.1574-0.1043-0.08870.19650.0613-0.13-0.0302-39.951125.053363.8997
11refined4.3311-4.5766-2.61015.62273.51755.9686-0.09580.1918-0.35440.48790.07960.06620.685-0.23540.01620.17780.17510.312-0.1335-0.1814-0.0882-11.230275.382460.7368
12refined3.7242-2.1179-0.56188.33351.89876.2445-0.05170.3671-0.1457-0.20550.02150.0180.06930.23680.0302-0.1947-0.1084-0.06350.1844-0.4428-0.095622.280220.7228-1.0401
142.38490.5484-0.91553.09851.16213.6597-0.1280.3406-0.0805-0.1213-0.086-0.00540.3065-0.41890.214-0.1833-0.08940.17130.056-0.2145-0.0663
153.6952-1.7612-1.62462.6712.73194.92320.05450.08370.2256-0.2070.1128-0.0925-0.6221-0.1739-0.16730.0869-0.05370.1646-0.1958-0.4293-0.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|601 - A|605 A|335 - A|545 }A601 - 605
2X-RAY DIFFRACTION1{ A|601 - A|605 A|335 - A|545 }A335 - 545
3X-RAY DIFFRACTION2{ B|601 - B|605 B|336 - B|362 B|365 - B|545 }B601 - 605
4X-RAY DIFFRACTION2{ B|601 - B|605 B|336 - B|362 B|365 - B|545 }B336 - 362
5X-RAY DIFFRACTION2{ B|601 - B|605 B|336 - B|362 B|365 - B|545 }B365 - 545
6X-RAY DIFFRACTION3{ C|601 - C|607 C|336 - C|366 C|372 - C|420 C|429 - C|545 }C601 - 607
7X-RAY DIFFRACTION3{ C|601 - C|607 C|336 - C|366 C|372 - C|420 C|429 - C|545 }C336 - 366
8X-RAY DIFFRACTION3{ C|601 - C|607 C|336 - C|366 C|372 - C|420 C|429 - C|545 }C372 - 420
9X-RAY DIFFRACTION3{ C|601 - C|607 C|336 - C|366 C|372 - C|420 C|429 - C|545 }C429 - 545
10X-RAY DIFFRACTION4{ D|601 - D|605 D|335 - D|541 }D601 - 605
11X-RAY DIFFRACTION4{ D|601 - D|605 D|335 - D|541 }D335 - 541
12X-RAY DIFFRACTION5{ E|601 - E|605 E|335 - E|366 E|371 - E|418 E|423 - E|428 }E601 - 605
13X-RAY DIFFRACTION5{ E|601 - E|605 E|335 - E|366 E|371 - E|418 E|423 - E|428 }E335 - 366
14X-RAY DIFFRACTION5{ E|601 - E|605 E|335 - E|366 E|371 - E|418 E|423 - E|428 }E371 - 418
15X-RAY DIFFRACTION5{ E|601 - E|605 E|335 - E|366 E|371 - E|418 E|423 - E|428 }E423 - 428
16X-RAY DIFFRACTION6{ F|601 - F|605 F|335 - F|542 }F601 - 605
17X-RAY DIFFRACTION6{ F|601 - F|605 F|335 - F|542 }F335 - 542
18X-RAY DIFFRACTION7{ G|158 - G|255 G|258 - G|292 }G158 - 255
19X-RAY DIFFRACTION7{ G|158 - G|255 G|258 - G|292 }G258 - 292
20X-RAY DIFFRACTION8{ H|158 - H|255 H|258 - H|292 }H158 - 255
21X-RAY DIFFRACTION8{ H|158 - H|255 H|258 - H|292 }H258 - 292
22X-RAY DIFFRACTION9{ I|158 - I|255 I|258 - I|292 }I158 - 255
23X-RAY DIFFRACTION9{ I|158 - I|255 I|258 - I|292 }I258 - 292
24X-RAY DIFFRACTION10{ J|158 - J|255 J|258 - J|292 }J158 - 255
25X-RAY DIFFRACTION10{ J|158 - J|255 J|258 - J|292 }J258 - 292
26X-RAY DIFFRACTION11{ K|157 - K|255 K|258 - K|292 }K157 - 255
27X-RAY DIFFRACTION11{ K|157 - K|255 K|258 - K|292 }K258 - 292
28X-RAY DIFFRACTION12{ L|158 - L|291 }L158 - 291

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