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- PDB-3h9z: Crystal structure of the IgE-Fc3-4 domains -

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Basic information

Entry
Database: PDB / ID: 3h9z
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: 2.45 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.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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4318
Polymers99,6814
Non-polymers2,7514
Water2,630146
1
A: Ig epsilon chain C region
B: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7513
Polymers49,8402
Non-polymers9111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-13.1 kcal/mol
Surface area22160 Å2
MethodPISA
2
C: Ig epsilon chain C region
D: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6805
Polymers49,8402
Non-polymers1,8403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-12.9 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.660, 99.352, 77.639
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT IS A DIMER. THE ASYMMETRIC UNIT CONTAINS 2 DIMERS (CHAINS A:B AND CHAINS C:D).

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Components

#1: Protein
Ig epsilon chain C region


Mass: 24920.146 Da / Num. of mol.: 4 / 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.: 3
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
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
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 of well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed ...Details: 1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter of 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: 2.45→30 Å / Num. all: 36017 / Num. obs: 36017 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.63 % / Rsym value: 0.059 / Net I/σ(I): 18.425
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.28 % / Rsym value: 0.241 / % possible all: 82.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.324 / Packing: 0.554
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: 2.45→28.71 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.504 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.619 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27748 1824 5.1 %RANDOM
Rwork0.22936 ---
obs0.23182 35946 98.75 %-
all-35946 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.21 Å2
2--0.55 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 184 146 6954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227068
X-RAY DIFFRACTIONr_bond_other_d0.0010.024938
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9889656
X-RAY DIFFRACTIONr_angle_other_deg0.7463.00311882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2822.267300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.975151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7581572
X-RAY DIFFRACTIONr_chiral_restr0.0830.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217608
X-RAY DIFFRACTIONr_gen_planes_other00.021412
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_it1.52224208
X-RAY DIFFRACTIONr_mcbond_other0.27721640
X-RAY DIFFRACTIONr_mcangle_it2.56936888
X-RAY DIFFRACTIONr_scbond_it1.39622860
X-RAY DIFFRACTIONr_scangle_it2.17932768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.582 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.395 226 -
Rwork0.326 4598 -
obs--91.61 %
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)
13.0575-0.7251-0.20462.8460.69042.6998-0.1752-0.0624-0.26880.19150.17410.10540.40110.1980.0011-0.04050.03740.09350.0159-0.0404-0.134896.9456-27.823237.2487
25.47578.73192.533613.92444.04031.1723-0.19350.05420.39920.09270.30650.46370.19020.072-0.11290.03870.01230.00940.1-0.04050.0461100.3596-9.019644.5183
34.4341-0.568-1.86021.96150.57783.7722-0.01330.07190.15890.0967-0.00190.0467-0.0552-0.02720.0151-0.08110.0084-0.0146-0.11570.0156-0.0342119.1932-11.95328.9467
42.6196-0.70040.10443.55080.04182.9987-0.0875-0.0439-0.16150.2282-0.09760.42520.004-0.37180.1851-0.0438-0.02110.0147-0.0717-0.0428-0.0199124.6938-37.591256.0347
51.76151.4751-4.8332.3016-5.433415.06230.0246-0.04390.0291-0.1267-0.1971-0.16120.0442-0.05260.17250.04420.0028-0.00880.0062-0.0096-0.0075133.8125-37.959237.7339
61.4176-0.80350.39242.99040.27621.9439-0.0217-0.07150.1227-0.04340.0251-0.1378-0.1572-0.0301-0.0034-0.04460.0193-0.0231-0.00950.0073-0.0563131.6502-13.848940.4927
73.50660.24010.80862.77011.45184.1099-0.0879-0.0498-0.32490.50320.07670.03860.59530.07640.0112-0.03520.03750.1293-0.0406-0.0013-0.078869.4723-31.71781.5571
88.597110.20350.183312.45460.83531.1112-0.1806-0.29790.4920.14060.06820.3529-0.0949-0.11130.1124-0.02730.02740.00830.0071-0.00680.007875.2368-13.20747.6054
92.2042-0.6383-0.60231.49260.51433.33480.049-0.0327-0.00440.0331-0.0087-0.00370.14220.0699-0.0403-0.04790.0079-0.0055-0.0701-0.0193-0.043892.0721-18.0068-9.6999
102.2319-0.0621-0.04663.86340.40822.6445-0.0668-0.182-0.0275-0.0377-0.23240.5213-0.0325-0.26590.2991-0.01250.0357-0.0414-0.091-0.1012-0.039898.181-41.795717.2143
115.50352.3465-8.72011.0005-3.71813.8168-0.0058-0.15230.3085-0.1001-0.0430.01120.1096-0.27880.04880.1310.0210.01250.01810.01530.0389107.4463-44.127-0.8667
121.738-0.66110.53954.09320.73282.3782-0.0197-0.0220.0718-0.0855-0.05140.0687-0.05420.11340.0711-0.06530.02070.0049-0.06310.011-0.1255105.2765-19.66071.1523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A336 - 433
2X-RAY DIFFRACTION2A434 - 440
3X-RAY DIFFRACTION3A441 - 544
4X-RAY DIFFRACTION4B1 - 5
5X-RAY DIFFRACTION4B336 - 433
6X-RAY DIFFRACTION5B434 - 440
7X-RAY DIFFRACTION6B441 - 544
8X-RAY DIFFRACTION7C1 - 5
9X-RAY DIFFRACTION7C336 - 433
10X-RAY DIFFRACTION8C434 - 440
11X-RAY DIFFRACTION9C441 - 544
12X-RAY DIFFRACTION10D1 - 5
13X-RAY DIFFRACTION10D336 - 433
14X-RAY DIFFRACTION11D434 - 440
15X-RAY DIFFRACTION12D441 - 544

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