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- PDB-3ha0: Crystal structure of the IgE-Fc3-4 domains -

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Basic information

Entry
Database: PDB / ID: 3ha0
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


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / 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 ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / 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 / molecular replacement / Resolution: 2.8 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _struct_conn.pdbx_leaving_atom_flag
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_role / _struct_conn.ptnr1_auth_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,98612
Polymers149,5216
Non-polymers5,4656
Water00
1
A: Ig epsilon chain C region
B: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6624
Polymers49,8402
Non-polymers1,8222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-13.9 kcal/mol
Surface area21980 Å2
MethodPISA
2
C: Ig epsilon chain C region
D: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6624
Polymers49,8402
Non-polymers1,8222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-10.2 kcal/mol
Surface area22790 Å2
MethodPISA
3
E: Ig epsilon chain C region
F: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6624
Polymers49,8402
Non-polymers1,8222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-12.4 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.900, 104.900, 150.000
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT IS A DIMER. THE ASYMMETRIC UNIT CONTAINS 3 DIMERS (CHAINS A:B, CHAINS C:D AND CHAINS E:F).

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Components

#1: Protein
Ig epsilon chain C region


Mass: 24920.146 Da / Num. of mol.: 6 / 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-(1-3)-[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-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

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed ...Details: 0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 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: 1.0001 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 7, 1999
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 37208 / Num. obs: 37208 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.073 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.4 % / Rsym value: 0.541 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.309 / Packing: 0.548
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å30 Ågeneral99.9 0

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FP5

1fp5


Resolution: 2.8→29.83 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU B: 40.643 / SU ML: 0.375 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Incorrect stereochemistry at C2 atom of MAN A 4.
RfactorNum. reflection% reflectionSelection details
Rfree0.28015 1860 5 %RANDOM
Rwork0.24144 ---
obs0.24339 36845 100 %-
all-36905 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.102 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å2-0.56 Å2
2--1.53 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9910 0 366 0 10276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210575
X-RAY DIFFRACTIONr_bond_other_d0.0010.027369
X-RAY DIFFRACTIONr_angle_refined_deg0.9081.98714449
X-RAY DIFFRACTIONr_angle_other_deg0.6163.00217741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.33951248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.10522.349447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.064151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.08515105
X-RAY DIFFRACTIONr_chiral_restr0.0530.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111397
X-RAY DIFFRACTIONr_gen_planes_other00.022106
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_it0.67226310
X-RAY DIFFRACTIONr_mcbond_other0.07122462
X-RAY DIFFRACTIONr_mcangle_it1.182310323
X-RAY DIFFRACTIONr_scbond_it0.47724265
X-RAY DIFFRACTIONr_scangle_it0.81634126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.954 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.395 222 -
Rwork0.324 4995 -
obs--100 %
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)
12.89210.60440.79163.3340.17172.9757-0.09980.06410.47250.34220.0428-0.0101-0.33840.16470.057-0.138-0.05090.0327-0.08230.0822-0.004522.507818.432721.5005
26.54374.84131.02313.58180.75690.16-0.06350.04050.3041-0.060.06580.13210.0691-0.0655-0.00230.0249-0.0013-0.02630.02330.0243-0.005813.9580.713621.8401
32.70770.05450.25462.6241-0.70614.57440.04010.00830.0447-0.23480.0747-0.1527-0.1353-0.0096-0.1148-0.0633-0.00670.0489-0.17970.1077-0.040810.12515.6341-2.6642
42.9801-1.1378-1.62363.74390.63011.8898-0.0076-0.6145-0.23630.544-0.0813-0.13940.0250.38880.08890.0726-0.0567-0.0381-0.1640.066-0.0135-10.084932.986314.2339
51.712-2.3429-6.39133.20628.746523.85990.33540.19760.42960.2027-0.1116-0.23860.4045-0.2089-0.22380.0810.0604-0.0167-0.02680.03410.0477-4.721733.2538-5.6406
62.72690.3185-0.25244.26990.18612.052-0.0839-0.00420.0099-0.12490.0253-0.0113-0.002-0.24290.0586-0.11660.0286-0.0072-0.0870.0586-0.0968-6.53168.8325-2.1155
74.37041.93110.74835.17432.22294.29720.2862-0.3197-0.6848-0.2381-0.1877-0.26250.66320.3823-0.09860.0925-0.0499-0.1102-0.15210.1015-0.2007-8.6954-32.580946.3221
820.406320.20729.514720.07049.09686.1876-0.0002-0.1669-0.60520.24730.1825-0.57970.07730.1616-0.18230.0399-0.0073-0.024800.01520.02471.4134-20.842559.5353
91.8382-0.1268-1.64493.6269-0.88145.79580.03210.32550.15880.01580.05130.04580.1281-0.5493-0.0833-0.2976-0.1101-0.04740.12230.0541-0.212-0.2886-5.47940.3935
105.029-0.090.82485.7382-2.71973.64630.3704-0.1519-0.5366-0.35370.15190.23221.0599-0.4265-0.52240.3662-0.0201-0.2178-0.3439-0.1121-0.300623.6525-32.073528.228
117.8922-12.68172.577220.3817-4.20571.93830.25410.20890.2382-0.2311-0.3166-0.73230.0576-0.17730.06240.0657-0.0221-0.04430.0589-0.0394-0.028414.7853-19.40315.1073
122.91590.06790.16842.4929-0.26025.15290.1446-0.26880.0588-0.0303-0.0544-0.03190.289-0.1587-0.0902-0.1237-0.0334-0.0101-0.08240.0387-0.149816.4812-5.539135.5227
130.38881.1549-0.25683.4309-0.7630.16970.04830.2444-0.2291-1.0967-0.0230.48390.0474-0.6034-0.02520.0310.0663-0.03820.5506-0.02580.348425.801930.605760.6318
1411.49716.0967-10.919913.1807-8.218310.96410.1072-0.09410.21120.3963-0.15070.2139-0.06560.38230.04350.0481-0.03870.0041-0.0056-0.04880.051321.1131.434581.345
156.4048-0.9166-1.17994.2769-0.91853.72580.2186-0.34560.30580.0254-0.0719-0.0098-0.13740.2851-0.1467-0.3571-0.05340.02280.0096-0.2019-0.180222.97596.68978.3505
163.14380.0336-0.06176.8628-0.89025.29510.26520.20621.1149-0.15710.0706-0.0386-0.9567-0.3163-0.3358-0.34410.08750.1220.1305-0.01050.2245-5.817917.707455.5956
1712.6383-10.3316-1.04318.46090.74060.9187-0.0699-1.52851.2759-0.44780.0371-0.61061.9968-0.57650.0328-0.0096-0.2139-0.14840.1686-0.1490.20212.1487-0.470354.9115
183.08760.00040.30973.03880.23196.0970.1011-0.18370.3290.37930.10220.19-0.07940.1047-0.2033-0.18650.01320.06480.0016-0.195-0.13266.19463.679879.1022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A336 - 433
2X-RAY DIFFRACTION1A1 - 5
3X-RAY DIFFRACTION2A434 - 440
4X-RAY DIFFRACTION3A441 - 544
5X-RAY DIFFRACTION4B336 - 433
6X-RAY DIFFRACTION5B434 - 440
7X-RAY DIFFRACTION6B441 - 544
8X-RAY DIFFRACTION7C336 - 433
9X-RAY DIFFRACTION7C1 - 5
10X-RAY DIFFRACTION8C434 - 440
11X-RAY DIFFRACTION9C441 - 544
12X-RAY DIFFRACTION10D336 - 433
13X-RAY DIFFRACTION10D1 - 5
14X-RAY DIFFRACTION11D434 - 440
15X-RAY DIFFRACTION12D441 - 544
16X-RAY DIFFRACTION13E336 - 433
17X-RAY DIFFRACTION13E1 - 5
18X-RAY DIFFRACTION14E434 - 440
19X-RAY DIFFRACTION15E441 - 544
20X-RAY DIFFRACTION16F336 - 433
21X-RAY DIFFRACTION16F1 - 5
22X-RAY DIFFRACTION17F434 - 440
23X-RAY DIFFRACTION18F441 - 544

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