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- PDB-4ki1: Primitive triclinic crystal form of the human IgE-Fc(epsilon)3-4 ... -

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Basic information

Entry
Database: PDB / ID: 4ki1
TitlePrimitive triclinic crystal form 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
Immunoglobulin heavy constant epsilon / Low affinity immunoglobulin epsilon Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDhaliwal, B. / Pang, M.O.Y. / Sutton, B.J. / Beavil, A.J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: A range of C3-C4 interdomain angles in IgE Fc accommodate binding to its receptor CD23.
Authors: Dhaliwal, B. / Pang, M.O. / Yuan, D. / Beavil, A.J. / Sutton, B.J.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_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_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.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 20, 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: LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
F: LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
G: LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
H: LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,98412
Polymers164,3418
Non-polymers3,6434
Water543
1
A: IG EPSILON CHAIN C REGION
B: IG EPSILON CHAIN C REGION
E: LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
F: LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9926
Polymers82,1704
Non-polymers1,8222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: IG EPSILON CHAIN C REGION
D: 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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.790, 63.840, 163.890
Angle α, β, γ (deg.)100.67, 90.13, 103.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
IG EPSILON CHAIN C REGION


Mass: 24920.146 Da / Num. of mol.: 4 / Fragment: HUMAN IGE-FC(EPSILON)3-4, UNP residues 209-428 / Mutation: N252Q, N264Q
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.: 4 / 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.: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26 % (w/v) PEG 1,500 and 20 % (v/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→80.4 Å / Num. all: 31141 / Num. obs: 30145 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.53 Å2
Reflection shellResolution: 3.2→3.37 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
BUSTER2.10.0refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EZM

4ezm


Resolution: 3.2→80.4 Å / Cor.coef. Fo:Fc: 0.8409 / Cor.coef. Fo:Fc free: 0.7907 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1523 5.05 %RANDOM
Rwork0.2325 ---
all0.2341 31141 --
obs0.2341 30144 96.79 %-
Displacement parametersBiso mean: 79.91 Å2
Baniso -1Baniso -2Baniso -3
1-6.3024 Å2-6.2953 Å2-3.3272 Å2
2---14.294 Å2-4.8153 Å2
3---7.9916 Å2
Refine analyzeLuzzati coordinate error obs: 0.752 Å
Refinement stepCycle: LAST / Resolution: 3.2→80.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10886 0 244 3 11133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00711480HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.915626HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d03948SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0244HARMONIC2
X-RAY DIFFRACTIONt_gen_planes01652HARMONIC5
X-RAY DIFFRACTIONt_it011480HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion1.7
X-RAY DIFFRACTIONt_other_torsion18.25
X-RAY DIFFRACTIONt_chiral_improper_torsion01544SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact011674SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2851 148 4.94 %
Rwork0.2508 2849 -
all0.2525 2997 -
obs--96.79 %
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)
13.78280.32931.29530.7470.04611.91120.31810.1774-0.0495-0.0240.03050.146-0.18820.0783-0.3486-0.29670.194-0.01280.0461-0.0168-0.2877-32.699-13.138484.1931
24.7343-0.7820.66620.506-0.52581.23230.3166-0.0112-0.1921-0.0709-0.1852-0.0011-0.15710.3445-0.1314-0.3006-0.0717-0.08590.2234-0.1948-0.317-9.4058-15.384696.3309
34.3610.6132-0.66743.5544-0.29531.26690.2489-0.60960.2076-0.1360.1072-0.07430.04620.1679-0.3561-0.591-0.00110.00570.2131-0.1086-0.5093-41.8205-27.382322.2151
45.1382-0.6614-0.96811.724-0.05811.35720.3185-0.24760.3291-0.1492-0.05920.30710.16590.0658-0.2594-0.5031-0.07040.0257-0.0623-0.1547-0.4234-18.3779-24.215910.1634
51.03890.87521.34060.81071.48312.56970.0003-0.1731-0.03590.0752-0.0721-0.0523-0.04870.09370.0719-0.10360.15610.06910.50910.12720.0304-45.0417-40.396555.3573
60.7484-0.3214-0.53710.23360.51382.01520.1017-0.1666-0.2591-0.11170.03260.0561-0.1259-0.1861-0.1344-0.0589-0.0517-0.08230.52850.20110.0038-15.0678-22.2694-25.3891
70.5879-0.124-0.1531.28960.12380.00650.0159-0.28-0.0763-0.08080.04710.00090.2815-0.1525-0.063-0.10190.151-0.10040.7955-0.1228-0.1931-35.8231-1.835250.3573
80.3519-0.01340.05070.25390.49454.26950.0383-0.19440.0740.16690.01350.01680.1704-0.0669-0.0517-0.2890.02660.12960.38550.13880.051-6.1774-15.3953131.7926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|336 - A|545 A|601 - A|605 }A336 - 545
2X-RAY DIFFRACTION1{ A|336 - A|545 A|601 - A|605 }A601 - 605
3X-RAY DIFFRACTION2{ B|335 - B|545 B|601 - B|605 }B335 - 545
4X-RAY DIFFRACTION2{ B|335 - B|545 B|601 - B|605 }B601 - 605
5X-RAY DIFFRACTION3{ C|335 - C|545 C|601 - C|605 }C335 - 545
6X-RAY DIFFRACTION3{ C|335 - C|545 C|601 - C|605 }C601 - 605
7X-RAY DIFFRACTION4{ D|336 - D|545 D|601 - D|605 }D336 - 545
8X-RAY DIFFRACTION4{ D|336 - D|545 D|601 - D|605 }D601 - 605
9X-RAY DIFFRACTION5{ E|158 - E|291 }E158 - 291
10X-RAY DIFFRACTION6{ F|158 - F|290 }F158 - 290
11X-RAY DIFFRACTION7{ G|158 - G|292 }G158 - 292
12X-RAY DIFFRACTION8{ H|159 - H|292 }H159 - 292

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