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- PDB-4gj0: Crystal structure of CD23 lectin domain mutant S252A -

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Basic information

Entry
Database: PDB / ID: 4gj0
TitleCrystal structure of CD23 lectin domain mutant S252A
ComponentsLow affinity immunoglobulin epsilon Fc receptor
KeywordsIMMUNE SYSTEM / Receptor
Function / homology
Function and homology information


low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / pattern recognition receptor activity / Fc-gamma receptor signaling pathway involved in phagocytosis / Interleukin-10 signaling ...low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / pattern recognition receptor activity / Fc-gamma receptor signaling pathway involved in phagocytosis / Interleukin-10 signaling / integrin binding / carbohydrate binding / protease binding / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / immune response / external side of plasma membrane / positive regulation of gene expression / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Low affinity immunoglobulin epsilon Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsYuan, D. / Sutton, B.J. / Dhaliwal, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Ca2+-dependent Structural Changes in the B-cell Receptor CD23 Increase Its Affinity for Human Immunoglobulin E.
Authors: Yuan, D. / Keeble, A.H. / Hibbert, R.G. / Fabiane, S. / Gould, H.J. / McDonnell, J.M. / Beavil, A.J. / Sutton, B.J. / Dhaliwal, B.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low affinity immunoglobulin epsilon Fc receptor
B: Low affinity immunoglobulin epsilon Fc receptor
C: Low affinity immunoglobulin epsilon Fc receptor
D: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34912
Polymers64,5964
Non-polymers7538
Water7,368409
1
A: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4334
Polymers16,1491
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4334
Polymers16,1491
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2412
Polymers16,1491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2412
Polymers16,1491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.501, 56.867, 62.680
Angle α, β, γ (deg.)68.060, 88.220, 73.530
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Low affinity immunoglobulin epsilon Fc receptor / BLAST-2 / C-type lectin domain family 4 member J / Fc-epsilon-RII / Immunoglobulin E-binding factor ...BLAST-2 / C-type lectin domain family 4 member J / Fc-epsilon-RII / Immunoglobulin E-binding factor / Lymphocyte IgE receptor / Low affinity immunoglobulin epsilon Fc receptor membrane-bound form / Low affinity immunoglobulin epsilon Fc receptor soluble form


Mass: 16148.986 Da / Num. of mol.: 4 / Fragment: UNP residues 156-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCER2, CD23A, CLEC4J, FCE2, IGEBF / Production host: Escherichia coli (E. coli) / References: UniProt: P06734
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 18.5% PEG 6000, 2% 1,6-hexanediol, 0.05M ammonium sulphate, 0.1M sodium acetate pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 46506 / Num. obs: 45157 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.94 Å2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 93.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H2R

2h2r


Resolution: 1.953→31.275 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8417 / SU ML: 0.24 / σ(F): 1.96 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2288 5.07 %random
Rwork0.1662 ---
all0.1685 46506 --
obs0.1685 45141 96.82 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.081 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 167 Å2 / Biso mean: 41.1362 Å2 / Biso min: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1--6.8445 Å2-2.5797 Å2-0.5192 Å2
2---3.7696 Å2-0.69 Å2
3---10.6141 Å2
Refinement stepCycle: LAST / Resolution: 1.953→31.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 44 409 4709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074438
X-RAY DIFFRACTIONf_angle_d1.0315988
X-RAY DIFFRACTIONf_chiral_restr0.076582
X-RAY DIFFRACTIONf_plane_restr0.004773
X-RAY DIFFRACTIONf_dihedral_angle_d13.3331563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.953-1.99510.35321280.26242400252888
1.9951-2.04150.2771430.24132650279395
2.0415-2.09250.28911450.21392660280596
2.0925-2.14910.24931470.20832644279197
2.1491-2.21230.2511500.19192690284097
2.2123-2.28370.2371360.18662716285297
2.2837-2.36530.23521490.17812702285198
2.3653-2.45990.24071380.17982678281697
2.4599-2.57180.24521400.18432704284498
2.5718-2.70740.27651370.1872748288598
2.7074-2.87690.25751480.17522708285698
2.8769-3.09880.21631270.1672752287998
3.0988-3.41030.20231480.16712683283198
3.4103-3.9030.20231490.14412743289298
3.903-4.91430.15821430.12292728287199
4.9143-31.2790.17211600.16272647280796
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)
10.5699-0.0475-0.0120.0212-0.0430.54750.1605-0.34910.04210.21440.0212-0.3298-0.3438-0.12620.13440.4251-0.12040.01670.3878-0.05090.2376-21.2042-18.96489.2431
20.48160.018-0.38920.31390.37541.29150.1611-0.11850.28690.2332-0.04080.1192-0.55470.0546-0.09570.3531-0.07930.08320.2521-0.06710.2626-23.2581-12.1321-4.5233
30.83530.18630.05750.5091-0.25230.06220.1955-0.41640.00210.22-0.1577-0.16270.02310.2620.01140.2683-0.08750.04610.2854-0.04230.1869-17.8526-17.0056-7.3451
40.09820.36620.00542.6551-0.47050.92940.0466-0.0858-0.10950.21650.18870.49340.1028-0.5278-0.09310.2716-0.05330.08080.3771-0.0050.3014-32.8417-20.88770.1608
50.8004-0.0173-0.1540.89850.06550.44280.00890.2931-0.2365-0.0783-0.00020.2585-0.0518-0.079-0.01740.23130.0123-0.01540.2575-0.02650.2088-24.4707-21.7727-14.9867
60.9836-0.09270.3890.312-0.42420.84070.2012-0.279-0.4359-0.1914-0.1455-0.08990.37940.2275-0.080.32110.0086-0.04820.2736-0.01580.2221-23.2152-29.0951-7.2185
72.2743-0.2106-0.2922.32440.58094.44730.10780.2625-0.0176-0.3411-0.24990.24090.2181-1.17750.05570.27-0.0406-0.07820.30920.00690.2545-33.5247-26.1829-19.1666
80.7169-0.3069-0.04050.2831-0.07031.050.13310.0117-0.0368-0.07390.07580.0836-0.1980.0234-0.06660.21890.01790.02840.19430.02280.2343-28.9107-17.775-17.1593
90.4961-0.0316-0.21150.73550.57690.70850.327-0.0124-0.01930.13620.1243-0.0658-0.0160.36350.35840.2973-0.09770.04750.2984-0.05770.161-18.8062-18.68514.8176
101.53131.1102-1.07666.0701-0.0490.8606-0.1490.4523-0.1726-0.44430.2238-0.4002-0.0948-0.3794-0.0690.36610.0443-0.01950.3758-0.08420.2953-7.9232-39.2594-43.5971
110.4646-0.3172-0.12860.7512-0.38391.0990.07590.27150.0743-0.1362-0.0888-0.35960.0504-0.1606-0.00010.23020.03620.00130.32760.01160.2229-6.2503-25.7946-38.322
121.23520.01040.31580.43720.43570.63090.20060.2886-0.2348-0.1283-0.17330.1569-0.0001-0.1865-0.01310.22210.0436-0.02670.2616-0.00590.1903-11.6629-27.3504-32.8945
130.17520.53150.03951.86450.23680.0595-0.1360.2533-0.27170.02960.2736-1.04580.25880.1037-0.05290.20340.02140.05570.2893-0.08470.38463.2848-35.3631-35.7231
141.41770.1117-0.21951.59640.01750.8288-0.03070.0510.143-0.489-0.0664-0.38920.04610.09530.03150.2607-0.02720.05380.26330.00420.2978-0.2811-23.6433-32.5733
155.2168-1.483-1.38554.9741.35560.5858-0.2467-0.755-0.03120.7178-0.12120.10130.36770.14950.17220.3529-0.05830.00750.374-0.01540.2491-9.0474-27.0889-16.8368
161.21970.574-0.32870.8316-0.15190.21270.2735-0.1259-0.18040.3483-0.0668-0.20770.16260.0846-0.09440.2771-0.0114-0.08880.2656-0.03410.2519-1.1032-31.08-21.3314
170.01460.0003-0.16011.06110.36411.280.0461-0.14960.03460.0254-0.0623-0.3103-0.09080.25550.01130.2182-0.03160.01970.251-0.01280.30220.7321-22.955-24.5293
180.8314-0.1886-0.14810.11990.02570.91660.0937-0.066-0.2863-0.06180.01220.2324-0.2034-0.02-0.06480.25270.01380.00950.21130.00530.2786-2.0339-18.994-26.2795
190.25380.2082-0.1021.07220.18870.78740.13590.1624-0.0045-0.3715-0.21760.0602-0.0345-0.4450.07580.33310.0388-0.02070.3582-0.07890.2076-10.7811-37.0417-40.5669
201.6560.9699-0.5961.4072-0.62071.5907-0.02370.09580.31550.16490.2956-0.0751-0.46470.3782-0.16980.5159-0.16680.12180.43580.04310.4261-17.71894.0498-43.9872
210.60360.3173-0.04281.1747-0.02472.51780.07970.16750.1744-0.16110.13470.1998-0.26570.43040.10680.2501-0.05490.00150.31830.06450.2272-22.8898-7.1417-39.7813
220.5145-0.1750.1131.0198-0.29431.50630.0793-0.0875-0.15580.00110.33060.7424-0.45280.17950.27610.0862-0.0037-0.09610.18480.0550.2252-31.3417-12.503-32.7306
231.51360.2313-0.25340.3474-0.53390.91810.19910.11450.24920.29610.39050.9747-0.3138-0.30730.08480.1654-0.0058-0.010.24010.10750.5038-36.0056-7.6156-32.7573
240.4254-0.1693-0.02771.2625-0.76451.89130.19720.1512-0.3104-0.02240.2290.99430.2043-0.3537-0.25920.23180.0386-0.0810.30810.09680.4226-34.4995-15.0784-37.17
250.056-0.15680.14183.9998-0.46020.6605-0.0095-0.0016-0.16310.07120.34940.85690.1317-0.1265-0.06390.25480.0009-0.11880.2301-0.00010.2706-30.5285-18.5626-37.2658
260.8078-0.34050.64130.145-0.270.43840.4707-0.15390.2718-0.1812-0.13710.1762-0.28790.6550.15310.4574-0.13630.16910.417-0.01130.2948-17.34680.3485-39.9944
270.4108-0.0685-0.33140.5880.43130.54650.07570.15930.4144-0.3427-0.20320.644-0.2042-0.1704-0.37220.41060.4306-0.013-0.20980.1621.257-11.212613.3733-21.2317
281.27130.2779-0.1170.1735-0.46771.90940.4838-0.04440.68890.1516-0.62730.1463-0.4404-0.1563-0.03740.43430.01920.11210.2617-0.05860.4214-8.83032.5724-12.5963
290.1213-0.1060.80584.1967-0.40215.16770.29360.19350.5624-0.0752-0.31850.90640.3794-1.3865-0.23250.15040.12180.02510.19850.02760.3558-9.2011-2.4493-18.5178
301.3830.085-0.08670.2941-0.99323.33240.1305-0.16440.99410.3358-0.4088-0.3584-1.01750.0590.1060.50850.01390.02280.2575-0.02370.73641.552110.7715-16.8518
310.87160.069-0.46551.44350.56541.35660.2117-0.1505-0.1172-0.2183-0.2522-0.296-0.40370.0387-0.00090.2243-0.0450.02470.22960.00950.29871.702-6.3802-17.0342
322.23821.6349-0.49311.53610.3161.6146-0.12860.5051-0.3129-0.05290.1801-0.1778-0.4575-0.4142-0.05110.27370.09-0.010.35030.00040.2669-0.1363-4.5984-26.1117
330.86480.0447-0.50390.60620.14380.31720.2206-0.3059-0.21730.0933-0.3688-0.5252-0.0860.23480.04940.2433-0.0148-0.01830.24250.0950.50217.8476-5.7055-17.0306
340.5962-0.54440.66372.31691.70043.74530.157-0.30240.14650.34290.0215-0.65440.25430.4375-0.11190.3191-0.0757-0.04680.29180.00030.45926.6117-0.2033-12.4539
351.13441.52990.61283.22370.17050.81970.5398-0.632-0.35320.7243-0.6282-0.42770.0853-0.2060.02620.3046-0.1287-0.03040.34120.03090.2343-1.9159-9.847-7.9564
360.2970.6472-0.38531.7239-0.62320.6170.34420.20640.440.0967-0.46690.5798-0.2686-0.32610.01340.34730.1793-0.01560.29990.04790.5435-10.75475.761-20.0248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 157:172)A157 - 172
2X-RAY DIFFRACTION2chain 'A' and (resseq 173:183)A173 - 183
3X-RAY DIFFRACTION3chain 'A' and (resseq 184:203)A184 - 203
4X-RAY DIFFRACTION4chain 'A' and (resseq 204:213)A204 - 213
5X-RAY DIFFRACTION5chain 'A' and (resseq 214:233)A214 - 233
6X-RAY DIFFRACTION6chain 'A' and (resseq 234:243)A234 - 243
7X-RAY DIFFRACTION7chain 'A' and (resseq 244:253)A244 - 253
8X-RAY DIFFRACTION8chain 'A' and (resseq 254:278)A254 - 278
9X-RAY DIFFRACTION9chain 'A' and (resseq 279:291)A279 - 291
10X-RAY DIFFRACTION10chain 'B' and (resseq 158:172)B158 - 172
11X-RAY DIFFRACTION11chain 'B' and (resseq 173:183)B173 - 183
12X-RAY DIFFRACTION12chain 'B' and (resseq 184:203)B184 - 203
13X-RAY DIFFRACTION13chain 'B' and (resseq 204:213)B204 - 213
14X-RAY DIFFRACTION14chain 'B' and (resseq 214:223)B214 - 223
15X-RAY DIFFRACTION15chain 'B' and (resseq 224:233)B224 - 233
16X-RAY DIFFRACTION16chain 'B' and (resseq 234:253)B234 - 253
17X-RAY DIFFRACTION17chain 'B' and (resseq 254:267)B254 - 267
18X-RAY DIFFRACTION18chain 'B' and (resseq 268:278)B268 - 278
19X-RAY DIFFRACTION19chain 'B' and (resseq 279:291)B279 - 291
20X-RAY DIFFRACTION20chain 'C' and (resseq 159:172)C159 - 172
21X-RAY DIFFRACTION21chain 'C' and (resseq 173:213)C173 - 213
22X-RAY DIFFRACTION22chain 'C' and (resseq 214:233)C214 - 233
23X-RAY DIFFRACTION23chain 'C' and (resseq 234:253)C234 - 253
24X-RAY DIFFRACTION24chain 'C' and (resseq 254:267)C254 - 267
25X-RAY DIFFRACTION25chain 'C' and (resseq 268:278)C268 - 278
26X-RAY DIFFRACTION26chain 'C' and (resseq 279:290)C279 - 290
27X-RAY DIFFRACTION27chain 'D' and (resseq 159:172)D159 - 172
28X-RAY DIFFRACTION28chain 'D' and (resseq 173:183)D173 - 183
29X-RAY DIFFRACTION29chain 'D' and (resseq 184:203)D184 - 203
30X-RAY DIFFRACTION30chain 'D' and (resseq 204:213)D204 - 213
31X-RAY DIFFRACTION31chain 'D' and (resseq 214:231)D214 - 231
32X-RAY DIFFRACTION32chain 'D' and (resseq 232:239)D232 - 239
33X-RAY DIFFRACTION33chain 'D' and (resseq 240:262)D240 - 262
34X-RAY DIFFRACTION34chain 'D' and (resseq 263:271)D263 - 271
35X-RAY DIFFRACTION35chain 'D' and (resseq 272:278)D272 - 278
36X-RAY DIFFRACTION36chain 'D' and (resseq 279:288)D279 - 288

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