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- PDB-2y7q: THE HIGH-AFFINITY COMPLEX BETWEEN IGE AND ITS RECEPTOR FC EPSILON RI -

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Basic information

Entry
Database: PDB / ID: 2y7q
TitleTHE HIGH-AFFINITY COMPLEX BETWEEN IGE AND ITS RECEPTOR FC EPSILON RI
Components
  • HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR SUBUNIT ALPHA
  • IG EPSILON CHAIN C REGION
KeywordsIMMUNE SYSTEM / ALLERGY / ANTIBODY / IGE-BINDING PROTEIN / HIGH-AFFINITY RECEPTOR / IMMUNOGLOBULIN C REGION
Function / homology
Function and homology information


high-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 / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation ...high-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 / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / antigen binding / 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 / cell surface receptor signaling pathway / inflammatory response / immune response / external side of plasma membrane / cell surface / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / 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 / High affinity immunoglobulin epsilon receptor subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsDavies, A.M. / Holdom, M.D. / Nettleship, J.E. / Beavil, A.J. / Owens, R.J. / Sutton, B.J.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Conformational Changes in Ige Contribute to its Uniquely Slow Dissociation Rate from Receptor Fceri
Authors: Holdom, M.D. / Davies, A.M. / Nettleship, J.E. / Bagby, S.C. / Dhaliwal, B. / Girardi, E. / Hunt, J. / Gould, H.J. / Beavil, A.J. / Mcdonnell, J.M. / Owens, R.J. / Sutton, B.J.
#1: Journal: Nat.Immunol. / Year: 2002
Title: The Crystal Structure of Ige Fc Reveals an Asymmetrically Bent Conformation.
Authors: Wan, T. / Beavil, R.L. / Fabiane, S.M. / Beavil, A.J. / Sohi, M.K. / Keown, M. / Young, R.J. / Henry, A.J. / Owens, R.J. / Gould, H.J. / Sutton, B.J.
History
DepositionFeb 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR SUBUNIT ALPHA
B: IG EPSILON CHAIN C REGION
D: IG EPSILON CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8447
Polymers94,4323
Non-polymers1,4124
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-14.8 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.491, 103.341, 110.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND RESID 337:364
211CHAIN D AND RESID 337:364
112CHAIN B AND RESID 371:377
212CHAIN D AND RESID 371:377
113CHAIN B AND RESID 391:437
213CHAIN D AND RESID 391:437
114CHAIN B AND RESID 438:448
214CHAIN D AND RESID 438:448
115CHAIN B AND RESID 462:544
215CHAIN D AND RESID 462:544

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR SUBUNIT ALPHA / HIGH AFFINITY IGE RECEPTOR FC EPSILON RI / IGE FC RECEPTOR SUBUNIT ALPHA / FC-EPSILON RI-ALPHA / FCERI


Mass: 21722.098 Da / Num. of mol.: 1 / Fragment: SOLUBLE EXTRACELLULAR DOMAINS, RESIDUES 26-201 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / References: UniProt: P12319
#2: Protein IG EPSILON CHAIN C REGION


Mass: 36354.781 Da / Num. of mol.: 2
Fragment: FC FRAGMENT COMPRISING DOMAINS CEPSILON2-4, RESIDUES 104-427
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): MOUSE MYELOMA NS0 / Production host: MUS MUSCULUS (house mouse) / References: UniProt: P01854
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 99 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 160 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ASN 99 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 160 TO ALA ENGINEERED RESIDUE IN CHAIN A, THR 167 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 105 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 146 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN 252 TO GLN ENGINEERED RESIDUE IN CHAIN D, CYS 105 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASN 146 TO GLN ENGINEERED RESIDUE IN CHAIN D, ASN 252 TO GLN
Sequence detailsCHAIN A RESIDUES -2 TO 0 ARTEFACT FROM PHLSEC VECTOR CHAIN A RESIDUES 177-179 ARTEFACT FROM PHLSEC ...CHAIN A RESIDUES -2 TO 0 ARTEFACT FROM PHLSEC VECTOR CHAIN A RESIDUES 177-179 ARTEFACT FROM PHLSEC VECTOR CHAIN A RESIDUES 180-185 C-TERMINAL HIS TAG CHAIN B RESIDUES 222-223 VECTOR LEADER SEQUENCE CHAIN D RESIDUES 222-223 VECTOR LEADER SEQUENCE SEQUENCE DISCREPANCIES ARE FOR THE SO-CALLED TRIPLE GLYCOSYLATION MUTANT. SEQUENCE DISCREPANCIES ARE FOR GLYCOLSYLATION AND DISULPHIDE BOND MUTANTS. CHAIN A V143A CLONING ARTIFACT.

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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: 3.78 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: SITTING DROP VAPOR DIFFUSION. RESERVOIR SOLUTION CONTAINED 2.8M SODIUM ACETATE PH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.4→37 Å / Num. obs: 16204 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 8.5
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1F6A AND 1O0V

1f6a

1o0v


Resolution: 3.4→37.68 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 27.55 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT MODELED.
RfactorNum. reflection% reflection
Rfree0.292 812 5 %
Rwork0.245 --
obs0.248 16116 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.81 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.972 Å20 Å20 Å2
2--8.9248 Å20 Å2
3----2.9528 Å2
Refinement stepCycle: LAST / Resolution: 3.4→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 92 0 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065500
X-RAY DIFFRACTIONf_angle_d1.1047497
X-RAY DIFFRACTIONf_dihedral_angle_d20.1031838
X-RAY DIFFRACTIONf_chiral_restr0.066866
X-RAY DIFFRACTIONf_plane_restr0.008951
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B206X-RAY DIFFRACTIONPOSITIONAL
12D206X-RAY DIFFRACTIONPOSITIONAL0.115
21B57X-RAY DIFFRACTIONPOSITIONAL
22D57X-RAY DIFFRACTIONPOSITIONAL0.079
31B331X-RAY DIFFRACTIONPOSITIONAL
32D331X-RAY DIFFRACTIONPOSITIONAL0.131
41B80X-RAY DIFFRACTIONPOSITIONAL
42D80X-RAY DIFFRACTIONPOSITIONAL0.081
51B395X-RAY DIFFRACTIONPOSITIONAL
52D395X-RAY DIFFRACTIONPOSITIONAL0.094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.61290.32991300.28062506X-RAY DIFFRACTION99
3.6129-3.89160.30561210.23232509X-RAY DIFFRACTION100
3.8916-4.28270.30131360.21712521X-RAY DIFFRACTION100
4.2827-4.90130.24341640.18672512X-RAY DIFFRACTION100
4.9013-6.17070.27151260.21152578X-RAY DIFFRACTION100
6.1707-37.68050.31681350.2732678X-RAY DIFFRACTION99

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