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- PDB-4gt7: An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a ... -

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Basic information

Entry
Database: PDB / ID: 4gt7
TitleAn engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor binding conformation
ComponentsIg epsilon chain C region
KeywordsIMMUNE SYSTEM / Immunoglobulin / antibody / IgE / Fc fragment / Fc receptor
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 / Resolution: 2.61 Å
AuthorsWurzburg, B.A. / Kim, B.K. / Jardetzky, T.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, nonreceptor binding conformation.
Authors: Wurzburg, B.A. / Kim, B. / Tarchevskaya, S.S. / Eggel, A. / Vogel, M. / Jardetzky, T.S.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
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_seq_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_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

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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)102,3618
Polymers98,8804
Non-polymers3,4814
Water2,270126
1
A: Ig epsilon chain C region
B: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2614
Polymers49,4402
Non-polymers1,8222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint19 kcal/mol
Surface area21700 Å2
MethodPISA
2
C: Ig epsilon chain C region
D: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0994
Polymers49,4402
Non-polymers1,6602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint16 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.753, 104.807, 45.899
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and resid 336:391) or (chain A and resid...
211(chain B and resid 336:391) or (chain B and resid...
311(chain C and resid 336:391) or (chain C and resid...
411(chain D and resid 336:391) or (chain D and resid...

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Components

#1: Protein
Ig epsilon chain C region


Mass: 24719.891 Da / Num. of mol.: 4
Fragment: IgE Fc Cepsilon3-Cepsilon4 fragment (unp residues 210-426)
Mutation: C328A, G335C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Trichoplusia ni (cabbage looper) / 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: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 20 mM sodium acetate, pH 4.6, 28.8% (w/v) PEG 4000, 2% (w/v) Anapoe -X-405, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.00757 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2004
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00757 Å / Relative weight: 1
ReflectionResolution: 2.61→30 Å / Num. all: 30718 / Num. obs: 29836 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 13.8
Reflection shellResolution: 2.61→2.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.99 / Rsym value: 0.354 / % possible all: 93.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→29.204 Å / SU ML: 0.36 / σ(F): 1.38 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 1395 4.68 %
Rwork0.1897 --
obs0.1924 29833 97.24 %
all-30718 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7573 Å2-0 Å23.4062 Å2
2---0.1393 Å20 Å2
3----1.6181 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6723 0 233 126 7082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097160
X-RAY DIFFRACTIONf_angle_d1.1949766
X-RAY DIFFRACTIONf_dihedral_angle_d22.752778
X-RAY DIFFRACTIONf_chiral_restr0.0681143
X-RAY DIFFRACTIONf_plane_restr0.0051227
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1495X-RAY DIFFRACTIONPOSITIONAL
12B1495X-RAY DIFFRACTIONPOSITIONAL0.06
13C1495X-RAY DIFFRACTIONPOSITIONAL0.062
14D1506X-RAY DIFFRACTIONPOSITIONAL0.061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6102-2.70350.32451860.26182626X-RAY DIFFRACTION92
2.7035-2.81160.3317930.25982849X-RAY DIFFRACTION98
2.8116-2.93950.29421860.23392805X-RAY DIFFRACTION98
2.9395-3.09430.3061930.23112915X-RAY DIFFRACTION98
3.0943-3.28790.30181860.21292792X-RAY DIFFRACTION98
3.2879-3.54140.27541860.19782817X-RAY DIFFRACTION98
3.5414-3.8970.2699930.18842901X-RAY DIFFRACTION98
3.897-4.45920.2271860.16212823X-RAY DIFFRACTION98
4.4592-5.61160.18431860.15462861X-RAY DIFFRACTION98
5.6116-29.20571000000000.17273049X-RAY DIFFRACTION97
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)
11.6330.2286-0.1530.38860.11540.78960.08670.1676-0.3052-0.22510.0085-0.0741-0.104-0.2905-0.11480.04240.0416-0.01630.15490.10250.064371.47227.117231.5997
20.53650.2592-0.05021.008-0.16612.112-0.1-0.00720.1261-0.1919-0.2357-0.0110.39630.14570.11630.20440.08490.01830.20880.09680.14654.7739.439560.2748
30.7578-1.890.8284.7476-2.23832.23130.11990.19240.4008-0.2447-0.9397-1.39650.08420.82460.60190.13670.09230.17850.36810.24140.373215.651415.745663.5579
40.96680.0427-0.1990.65340.07420.4881-0.0984-0.0072-0.3345-0.2068-0.0041-0.0432-0.01180.01440.12070.13140.00770.0710.13530.04370.19015.45732.028932.6235
50.76410.4122-0.41780.44920.16191.07990.00520.0572-0.1290.0612-0.143-0.06820.1232-0.21080.13180.1265-0.07840.02210.12190.00570.191548.569211.217136.5228
61.0685-0.7129-0.86870.87530.34751.4694-0.17260.13450.01920.2679-0.0998-0.05190.291-0.28380.24910.1726-0.10740.08220.1856-0.0320.15242.502415.04752.4797
70.67790.31160.24760.80590.22260.89970.07880.0138-0.12930.1356-0.26960.06870.1896-0.07740.05440.1982-0.07870.03660.1234-0.04490.1617-7.796529.192854.8874
80.57240.17980.41410.6610.51551.5796-0.16750.0946-0.20620.01930.076-0.1259-0.0980.24140.06880.0501-0.03210.00530.09630.01360.1188-10.64724.621838.2136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 336:435)
2X-RAY DIFFRACTION2(chain B and resid 336:435)
3X-RAY DIFFRACTION3(chain C and resid 336:435)
4X-RAY DIFFRACTION4(chain D and resid 336:435)
5X-RAY DIFFRACTION5(chain A and resid 440:541)
6X-RAY DIFFRACTION6(chain B and resid 440:541)
7X-RAY DIFFRACTION7(chain C and resid 440:541)
8X-RAY DIFFRACTION8(chain D and resid 440:541)

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