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- PDB-4grg: Crystal structure of IgE complexed with E2_79, an anti-IgE inhibitor -

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Basic information

Entry
Database: PDB / ID: 4grg
TitleCrystal structure of IgE complexed with E2_79, an anti-IgE inhibitor
Components
  • ANTI-IGE INHIBITOR E2_79
  • Ig epsilon chain C region
KeywordsIMMUNE SYSTEM/INHIBITOR / Ig-fold / immunity / high/low affinity receptor / IMMUNE SYSTEM-INHIBITOR complex
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 / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / immunoglobulin complex, circulating / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / inflammatory response / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Ankyrin repeats (many copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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
Similarity search - Domain/homology
Anti-ige inhibitor e2_79 / Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.24 Å
AuthorsKim, B. / Jardetzky, T.S.
CitationJournal: Nature / Year: 2012
Title: Accelerated disassembly of IgE-receptor complexes by a disruptive macromolecular inhibitor.
Authors: Kim, B. / Eggel, A. / Tarchevskaya, S.S. / Vogel, M. / Prinz, H. / Jardetzky, T.S.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-IGE INHIBITOR E2_79
B: ANTI-IGE INHIBITOR E2_79
C: Ig epsilon chain C region
D: Ig epsilon chain C region


Theoretical massNumber of molelcules
Total (without water)80,5704
Polymers80,5704
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.315, 71.315, 178.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resseq 333:392 or resseq 394:423 or resseq...
211chain D and (resseq 333:392 or resseq 394:423 or resseq...
112chain A and (resseq 12:135 )
212chain B and (resseq 12:135 )

NCS ensembles :
ID
1
2
DetailsOne biological assembly consisting of one IgE-Fc and two E2_79 is observed in an asymmetric unit.

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Components

#1: Protein ANTI-IGE INHIBITOR E2_79


Mass: 14647.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: L7MTK7*PLUS
#2: Protein Ig epsilon chain C region


Mass: 25637.812 Da / Num. of mol.: 2 / Fragment: IG-LIKE DOMAINS 3 AND 4, RESIDUES 210-428 / Mutation: G216C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01854

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Phosphate-citrate pH 4.2, 5% (w/v) PEG-3000, 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2010
RadiationMonochromator: Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 4.24→178.52 Å / Num. all: 9512 / Num. obs: 8467 / % possible obs: 89.01 % / Observed criterion σ(I): -3
Reflection shellResolution: 4.24→4.31 Å / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.24→29.753 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.887 / SU ML: 1.43 / σ(F): 1.96 / Phase error: 40.07 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NATIVE DATA WERE SUBMITTED TO THE DIFFRACTION ANISOTROPY SERVER, WHICH INDICATED SIGNIFICANT ANISOTROPY WITH PRINCIPLE COMPONENTS OF 20. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NATIVE DATA WERE SUBMITTED TO THE DIFFRACTION ANISOTROPY SERVER, WHICH INDICATED SIGNIFICANT ANISOTROPY WITH PRINCIPLE COMPONENTS OF 20.6 X 20.5 X -41.2 (ANGSTROM2) ALONG THE A*. B* AND C* AXES. THE DATA WERE TRUNCATED TO 4.2 ANGSTROM ALONG THE C* AXIS AND 4.5 ANGSTROM ALONG THE A*/B* AXES.
RfactorNum. reflection% reflection
Rfree0.3378 303 4.74 %
Rwork0.2704 --
obs0.2734 6399 89.17 %
all-9512 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 225.985 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.63 Å20 Å2-0 Å2
2--7.63 Å20 Å2
3----13.7428 Å2
Refinement stepCycle: LAST / Resolution: 4.24→29.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 0 0 5154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125273
X-RAY DIFFRACTIONf_angle_d1.3977183
X-RAY DIFFRACTIONf_dihedral_angle_d16.1191898
X-RAY DIFFRACTIONf_chiral_restr0.081823
X-RAY DIFFRACTIONf_plane_restr0.006942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1629X-RAY DIFFRACTIONPOSITIONAL
12D1629X-RAY DIFFRACTIONPOSITIONAL0.272
21A891X-RAY DIFFRACTIONPOSITIONAL
22B891X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2404-5.33750.37481470.3032699X-RAY DIFFRACTION79
5.3375-29.75410.32491560.26033397X-RAY DIFFRACTION99
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)
12.1177-6.7015-4.78774.0326-0.12882.00650.6931-3.2331-4.84462.1986-3.49381.79112.92231.3135-3.05713.455-0.63440.5621.1846-0.4682.6064-3.60377.4162-29.0708
25.91860.6389-3.8963-0.1218-0.72654.99810.0621-1.79183.0425-0.81410.23471.5731-0.84792.948702.2217-0.2617-0.00672.0206-0.52452.1918-9.5557.538-30.0495
31.4458-2.6975-0.52624.6409-0.1741-0.22881.39481.0033-2.31283.4554-3.3505-2.71811.1203-5.68670.0672.357-0.8683-0.82831.8479-0.95452.0446-18.44716.7199-26.5684
42.0206-1.9822-1.2131.18521.18721.0581-0.22443.18471.3951-2.08950.9156-2.59252.7885-2.91960.02352.4735-0.72930.02223.2088-0.29893.5034-27.18612.0576-22.9586
50.3683-0.39890.29160.2359-0.35920.44262.6416-4.646-0.63932.44944.86361.79954.278-0.77480.08956.6939-1.44640.52773.8464-0.98083.3565-33.53458.1131-17.4755
64.12976.7358-4.77631.90012.04529.27013.86021.077-2.23111.968-1.25062.03971.14112.5688-0.29633.44081.471-0.46271.2311-0.51783.3668-4.567430.281432.9824
72.1338-1.32292.8496.6685-1.43552.4505-2.2416-0.59722.103-1.3217-0.874-1.5861-0.3256-0.6414-0.02032.21060.41140.34111.9041-0.71882.6121-15.134735.440731.4223
83.15582.68435.31483.32552.52291.92993.9207-5.001-0.38052.08891.4082-1.9672.1262-6.78620.99351.00321.14750.2832.0844-1.2814.5721-27.226639.158926.4735
90.8432-1.47051.7672.8714-3.49323.91318.09251.58882.2497-2.74092.66263.832-1.1029-2.01590.53915.61910.09140.76472.807-0.66264.1911-33.581833.025521.0858
107.4451-0.01262.35993.88013.92982.69792.1061.0967-0.86581.0936-2.2210.95640.9017-0.8582-0.12763.02010.93160.51362.23710.46091.8271-11.959437.38255.6445
118.56951.5552-6.24710.8198-0.23464.6715-0.39571.5306-0.1117-0.2428-0.3615-0.8440.0471-1.2018-02.93070.78890.30841.77930.16582.4229-12.433738.49664.6087
120.97290.66110.66535.8317-4.65784.5360.2885-0.91774.41332.40450.45143.3491-1.5641-1.2320.55332.20950.55631.03542.11740.72583.0289-13.023731.556512.3471
139.9219-3.6744-3.377210.686-1.82217.1793-0.0987-0.48710.92780.1565-0.34850.1522-2.02871.1611-0.00091.9588-0.61120.04721.92660.27321.559214.36529.22951.5198
142.6026-2.2218-4.87156.84740.6956.0070.6755-1.2903-2.5281-1.6106-2.3764.1733-2.0385-0.6797-0.60893.4685-1.1727-0.31721.88880.541.0135-11.87643.5478-2.4465
1510.15552.77617.24730.26793.38624.8185-0.7306-1.7317-0.2311-0.5254-0.24670.6382-0.2504-2.691-0.00042.9817-0.3062-0.15271.88750.30022.3422-12.2942.6879-1.5235
160.9207-1.2852.98948.9894-4.92777.9694-0.81-1.9349-3.143-0.45330.74542.08372.2043-2.4690.11442.6512-0.6743-0.41762.4030.56322.499-12.93589.8168-8.7096
1710.49962.46145.42917.90180.41093.3015-0.11250.0714-0.1846-0.166-0.3815-0.13072.18991.4624-0.00042.18640.1979-0.00942.0530.31331.686114.325511.95032.0001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 12:24)
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:56)
3X-RAY DIFFRACTION3chain 'A' and (resseq 57:92)
4X-RAY DIFFRACTION4chain 'A' and (resseq 93:122)
5X-RAY DIFFRACTION5chain 'A' and (resseq 123:135)
6X-RAY DIFFRACTION6chain 'B' and (resseq 12:32)
7X-RAY DIFFRACTION7chain 'B' and (resseq 33:92)
8X-RAY DIFFRACTION8chain 'B' and (resseq 93:122)
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:135)
10X-RAY DIFFRACTION10chain 'C' and (resseq 332:384)
11X-RAY DIFFRACTION11chain 'C' and (resseq 385:421)
12X-RAY DIFFRACTION12chain 'C' and (resseq 422:443)
13X-RAY DIFFRACTION13chain 'C' and (resseq 444:545)
14X-RAY DIFFRACTION14chain 'D' and (resseq 333:384)
15X-RAY DIFFRACTION15chain 'D' and (resseq 385:421)
16X-RAY DIFFRACTION16chain 'D' and (resseq 422:443)
17X-RAY DIFFRACTION17chain 'D' and (resseq 444:545)

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