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- PDB-2wqr: The high resolution crystal structure of IgE Fc -

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Basic information

Entry
Database: PDB / ID: 2wqr
TitleThe high resolution crystal structure of IgE Fc
ComponentsIG EPSILON CHAIN C REGION
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / type 2 immune response / immunoglobulin receptor binding / immunoglobulin complex, circulating / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / FCERI mediated MAPK activation / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / 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: 1.9 Å
AuthorsDhaliwal, B. / Sutton, B.J. / Beavil, A.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
DepositionAug 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,56712
Polymers71,8612
Non-polymers2,70610
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-46.3 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.502, 75.282, 79.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein IG EPSILON CHAIN C REGION / IMMUNOGLOBULIN E / IGE FC


Mass: 35930.289 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT, RESIDUES 105-427 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE6 / Cell line (production host): MOUSE MYELOMA NS0 / Production host: MUS MUSCULUS (house mouse) / 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.: 2
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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Non-polymers , 5 types, 541 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 146 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 252 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN 146 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 252 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN 146 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN 252 TO GLN
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 291 K / pH: 8.5
Details: THE PROTEIN CONCENTRATION WAS 1.9 MG/ML. CRYSTALS GREW AT 18 DEGREES C WITH 14% PEG 8000, 200MM LITHIUM SULPHATE, 100MM TRIS-HCL PH 8.5 AS PRECIPITANT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 62035 / % possible obs: 99.9 % / Observed criterion σ(I): 1.33 / Redundancy: 7.3 % / Biso Wilson estimate: 31.56 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000- DENZOdata reduction
HKL-2000- SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O0V

1o0v


Resolution: 1.9→36 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 23.7 / Stereochemistry target values: ML
Details: RESIDUE 318, 319 AND 367 ARE DISORDERED IN CHAIN B. THE OCCUPANCY WAS SET TO ZERO FOR THE DISORDERED REGIONS.
RfactorNum. reflection% reflection
Rfree0.234 3120 5 %
Rwork0.1928 --
obs0.1949 61875 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.155 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 47.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.3857 Å20 Å20 Å2
2--3.3369 Å20 Å2
3----1.9512 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 175 533 5725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055326
X-RAY DIFFRACTIONf_angle_d1.0017255
X-RAY DIFFRACTIONf_dihedral_angle_d21.4572000
X-RAY DIFFRACTIONf_chiral_restr0.066841
X-RAY DIFFRACTIONf_plane_restr0.004931
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)
11.307-0.03140.18720.5335-0.08830.29570.0515-0.0677-0.19030.04630.01190.0911-0.0806-0.0023-0.04760.1472-0.0331-0.03420.17030.00450.150218.474412.799458.0232
27.8348-4.54211.92475.1403-0.30162.91640.0651-0.0272-0.81080.22850.15870.89440.6299-0.1743-0.24740.2477-0.0187-0.01070.13160.04520.226421.86432.482564.4219
3-0.07670.0256-0.19730.1043-0.05221.683-0.064-0.06070.03690.0306-0.02570.0199-0.3359-0.11530.07320.1989-0.0346-0.04540.15480.02520.141416.088919.347157.0255
40.926-0.3637-1.05241.00651.3056-3.15560.37430.30640.0373-0.427-0.244-0.0563-0.01-0.2996-0.09590.30810.06810.0080.2830.03820.115123.399519.890442.6617
50.717-0.3226-0.12451.2754-0.55221.7880.12150.11620.1270.12230.421-0.2462-0.78670.0099-0.42740.4637-0.02850.18720.15350.00110.348135.817620.093628.8014
60.87740.0586-0.5317-3.34871.58581.84640.7244-0.26261.1274-0.23710.65-0.5349-1.58360.3039-0.72080.8912-0.09460.31390.0460.19230.410734.32226.048629.9699
72.6612-1.13810.4681-0.51040.07871.82170.2531-0.32520.3751-0.0750.1449-0.3061-0.4221-0.0725-0.33240.4473-0.07160.07050.1837-0.02820.292933.351619.231137.4877
82.5416-0.51430.66821.08740.49750.75560.06210.1720.2958-0.0196-0.1744-0.0610.111-0.01570.0880.13670.0130.0070.12310.02380.160738.0564-1.471714.2062
90.747-1.251.82521.22372.05296.4432-0.1392-0.20860.27950.2614-0.1789-0.07260.2339-0.88270.3320.15-0.00480.01380.2482-0.0630.177828.30430.122420.9583
101.6135-0.41350.44470.44430.09822.15380.04530.3210.41110.0319-0.2303-0.20090.23760.14210.10820.15510.04130.02640.17830.07210.172144.3023-3.675313.1468
110.64610.84060.27771.44330.64760.87130.2609-0.0595-0.03760.2541-0.38630.0652-0.016-0.290.11960.2014-0.0559-0.00090.2956-0.03970.166715.77636.9547.6463
122.3989-1.7782-2.7717-1.2171.05767.8314-0.0442-0.0517-0.6757-0.2137-0.4180.41290.41130.08470.43440.4198-0.11850.01510.1568-0.03140.300813.7807-5.162943.4467
131.0967-0.3996-0.00842.4232.3930.56860.09660.1958-0.2959-0.2861-0.39030.16220.16210.01350.2070.2555-0.0142-0.01770.2405-0.06050.244714.72881.097243.0515
140.46391.4530.47681.85280.17010.95160.0866-0.4537-0.26870.1471-0.2705-0.3898-0.01680.27720.12430.0967-0.0317-0.02930.28440.02960.24058.33439.82299.4154
152.5559-0.3627-0.80860.23110.18920.12030.0341-0.54730.16430.0160.0932-0.11290.0180.1391-0.09360.1670.0143-0.03030.295-0.01510.1893-0.860216.947410.9702
162.0408-0.20731.15320.14380.5827-4.0536-0.1435-0.76310.03920.19820.0719-0.10340.2406-1.1307-0.01790.2585-0.0068-0.09220.569-0.01270.1509-1.488512.292322.2988
170.077-0.2930.02651.0577-0.11470.285-0.0325-0.19170.0608-0.0368-0.0628-0.2429-0.07850.09250.0710.141-0.00570.00610.2434-0.02650.21383.145319.15626.8627
180.6476-0.16310.4240.9276-0.0220.33540.06290.01880.07840.14340.0553-0.0075-0.00680.022-0.10060.15920.0233-0.0140.20790.04020.158825.4597-4.36548.9711
190.9006-0.14660.95780.2427-0.40950.5792-0.0739-0.1210.094-0.0193-0.02460.0454-0.2037-0.06050.07660.18990.02390.01130.18150.00050.134519.0121-3.131911.1085
201.55540.21190.56940.123-0.01470.48850.11420.1399-0.0944-0.00790.02540.04090.09820.0297-0.1060.16250.02640.0060.16170.0160.165620.7205-10.2028.075
211.7416-1.3539-0.9547-1.35013.2737-2.4645-0.3609-1.1650.33040.2842-0.2007-0.23640.3548-0.210.3350.31210.1289-0.02830.71850.04510.222311.196612.902320.3834
223.8934-1.1031.1296-1.27274.2664-4.7256-0.15361.6913-0.0799-0.6566-0.3702-0.0034-0.9018-0.24850.2981.0952-0.04790.15620.79920.10060.493125.602517.265122.2454
230.70020.02580.15580.4074-0.2850.09050.2641-0.1398-0.3010.24140.140.0302-0.0773-0.3806-0.20020.67770.03140.19640.6322-0.13140.687123.15896.969831.403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 228:282)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 283:298)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 299:320)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 321:344)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 345:374)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 375:401)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 402:439)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 440:492)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 493:510)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 511:547)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 228:253)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 254:278)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 279:335)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 336:353)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 354:385)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 386:401)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 402:437)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 438:478)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 479:503)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 504:548)
21X-RAY DIFFRACTION21(CHAIN C)
22X-RAY DIFFRACTION22(CHAIN D)
23X-RAY DIFFRACTION23(CHAIN E)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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