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- PDB-4g9a: Crystal structure of calcium2+-bound wild-type CD23 lectin domain -

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Basic information

Entry
Database: PDB / ID: 4g9a
TitleCrystal structure of calcium2+-bound wild-type CD23 lectin domain
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 / Interleukin-10 signaling / Fc-gamma receptor signaling pathway involved in phagocytosis ...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 / Interleukin-10 signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / 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: 2.001 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
DepositionJul 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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)65,09711
Polymers64,6604
Non-polymers4377
Water7,278404
1
A: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2973
Polymers16,1651
Non-polymers1322
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)16,2973
Polymers16,1651
Non-polymers1322
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)16,2052
Polymers16,1651
Non-polymers401
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)16,2973
Polymers16,1651
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.243, 53.705, 56.641
Angle α, β, γ (deg.)112.920, 88.530, 114.960
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: 16164.986 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: CD23A, CLEC4J, FCE2, FCER2, 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2010
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 35333 / Num. obs: 34951 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.96 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 96.9

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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: 2.001→38.839 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8687 / SU ML: 0.25 / σ(F): 1.96 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 1732 5.01 %RANDOM
Rwork0.1524 ---
all0.155 35333 --
obs0.155 34538 97.32 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.879 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 136.83 Å2 / Biso mean: 26.6003 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.0884 Å2-2.6684 Å22.9653 Å2
2--1.2913 Å2-1.3292 Å2
3----1.3797 Å2
Refinement stepCycle: LAST / Resolution: 2.001→38.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 22 404 4653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064443
X-RAY DIFFRACTIONf_angle_d0.9636007
X-RAY DIFFRACTIONf_chiral_restr0.069587
X-RAY DIFFRACTIONf_plane_restr0.004780
X-RAY DIFFRACTIONf_dihedral_angle_d12.5941595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0012-2.06010.26041260.20592543266991
2.0601-2.12660.21931310.18762719285097
2.1266-2.20260.22971470.16092726287397
2.2026-2.29070.24691380.15642728286697
2.2907-2.3950.22641500.15542732288297
2.395-2.52120.211500.15992764291498
2.5212-2.67920.25391490.16442760290998
2.6792-2.8860.23361490.15992743289298
2.886-3.17630.20341610.14392775293698
3.1763-3.63560.21361300.1412777290799
3.6356-4.57930.15191610.1262749291099
4.5793-38.84650.18781400.15752790293099
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)
10.380.05380.06860.23260.20430.39590.0359-0.0397-0.05720.0252-0.0430.05030.0578-0.08140.01820.0874-0.00040.00590.10320.00030.0778-16.570224.2365-12.8586
20.8259-0.00590.54240.23090.04410.59990.1527-0.0142-0.0719-0.1304-0.0151-0.09820.0573-0.0964-0.06410.10730.0176-0.00670.1001-0.02270.1212-15.567435.7524-19.2192
30.4373-0.31210.12510.9861-0.7361.1564-0.26010.12840.0605-0.1194-0.2952-0.382-0.12680.4301-0.72380.05350.07380.1232-0.0926-0.1868-0.0361-12.082123.6512-27.7574
40.5202-0.15490.15240.32180.17410.55070.02030.03770.0211-0.0318-0.01990.0179-0.0162-0.07240.00750.1010.00560.00910.1001-0.00430.0945-9.304124.2175-22.3776
50.63680.3831-0.19170.47-0.31320.2289-0.11190.2154-0.0148-0.33910.1085-0.04580.293-0.13280.00960.2372-0.08520.02280.2435-0.01490.1524-31.708942.3915-50.0456
60.1623-0.05730.17290.1414-0.00890.90980.110.0311-0.0331-0.01380.03360.01340.07840.1962-0.03050.1328-0.00930.01710.1482-0.00580.154-26.434543.3564-37.898
70.85110.3014-0.0330.6094-0.94161.7171-0.23450.09940.05230.0388-0.0162-0.1503-0.2801-0.01280.11770.1278-0.0235-0.01260.1241-0.01580.1509-25.329852.3023-34.6534
80.1815-0.2552-0.14540.35540.20880.1979-0.01090.09310.1745-0.12340.1419-0.0705-0.13710.06160.05890.0691-0.0709-0.03990.14620.01510.0248-35.224147.6963-39.0881
91.29120.52740.16860.539-0.27841.22690.10920.0509-0.0156-0.12370.05170.03550.3233-0.1675-0.04360.173-0.04230.02180.1573-0.01910.1634-37.255235.6538-39.5763
101.03830.54460.23990.61310.28931.3950.07130.0023-0.3302-0.02840.0483-0.06790.1145-0.0491-0.06180.15810.0185-0.0280.1021-0.01530.1464-29.225239.1828-30.7072
110.1358-0.0731-0.01990.03940.00380.0456-0.0989-0.21740.11290.1696-0.03640.171-0.067-0.2133-0.0302-0.0230.22850.24050.0711-0.2878-0.2113-38.985854.9063-25.3079
120.14120.1731-0.15610.7518-0.14140.1718-0.03930.06750.2245-0.0621-0.06020.1587-0.00090.0044-0.07850.06010.2708-0.0445-0.01360.1070.1216-40.693351.8598-33.5065
130.4570.13180.17820.74830.3810.23640.0333-0.03620.13920.2396-0.08150.04420.1926-0.32630.0130.1473-0.0220.01870.23260.00090.12-39.822944.5612-23.8452
140.57740.46640.35291.37461.25461.19770.00390.0684-0.20820.22040.0471-0.05750.2122-0.0369-0.02820.1321-0.03620.01170.1095-0.00690.1569-36.305538.4353-26.479
150.2129-0.05520.05850.0412-0.0440.10940.0388-0.02330.0919-0.0510.0323-0.06130.0415-0.0241-0.00570.15770.0113-0.04990.17040.03380.1151-26.35246.1275-22.554
160.0305-0.0992-0.02330.3748-0.0380.2455-0.1120.3052-0.0301-0.04260.1931-0.22980.0475-0.1027-0.02320.0957-0.05710.03620.2432-0.01820.1268-31.201146.7717-46.5154
171.3933-0.196-0.1220.2886-0.01730.1587-0.1102-0.099-0.1552-0.09840.0228-0.111-0.22340.3692-0.00720.2457-0.1022-0.0190.2751-0.0120.2029-9.248958.0878-1.3798
180.13620.03760.12410.25970.05810.1064-0.0875-0.01170.01440.19670.0231-0.0316-0.219-0.01950.00150.18070.023-0.0220.11190.00670.0882-21.613654.1321-3.5458
190.0749-0.02040.07660.3233-0.06740.148-0.0197-0.0034-0.0530.02470.06110.00330.043-0.06590.01680.139-0.0122-0.03320.11250.01510.1008-27.684541.0406-8.743
200.1710.06030.02830.15720.12720.24730.0740.0110.03030.1338-0.04660.0447-0.13610.10510.05660.16380.025-0.02130.16470.02210.0971-24.47851.7029-3.4997
210.5355-0.1657-0.16350.4217-0.14630.15760.0945-0.2759-0.52230.0913-0.0178-0.19210.09210.0678-0.01640.17970.0025-0.04750.19360.06320.39410.062348.9592-22.5128
220.73090.01010.2640.24570.11390.40810.0256-0.0596-0.3582-0.0854-0.0117-0.2047-0.0337-0.0144-0.00050.0928-0.0171-0.01230.10330.0040.1784-12.364953.5308-30.2437
230.1756-0.0913-0.17370.21780.21280.27760.2708-0.1863-0.262-0.0030.02360.00370.1595-0.08970.04680.1215-0.0148-0.08840.11180.05490.1519-7.018458.9477-24.1354
240.1989-0.06470.33180.193-0.22980.8516-0.17830.1905-0.05780.0324-0.208-0.2428-0.00860.16850.14350.121-0.02120.0320.19030.00980.32613.461659.8872-30.322
250.1895-0.041-0.07710.0278-0.02020.1242-0.01850.1658-0.1565-0.23080.1582-0.1417-0.02830.1195-0.00580.1507-0.01350.06760.1257-0.04280.1659-6.881559.4904-37.9266
261.72560.3803-0.10150.23490.17771.66390.1137-0.08760.34220.0165-0.00070.0712-0.21570.0112-0.0710.1578-0.01740.00480.12810.00080.1837-16.590573.5135-27.0859
272.7996-0.792-0.29651.02090.17390.7940.0202-0.19610.33370.0810.1698-0.16410.14940.2508-0.05150.14020.06-0.02110.2268-0.02090.1698-10.92167.2359-22.6788
280.36440.0046-0.04780.71920.15090.03630.12260.14520.37-0.018-0.0212-0.2539-0.0935-0.02260.00490.162-0.01520.01630.13690.0630.2728-3.134571.8931-31.2834
290.12620.0645-0.01720.1361-0.22590.639-0.04760.19220.28160.01110.00320.0366-0.1991-0.131-0.01190.1458-0.0038-0.02170.10050.03270.1646-13.657872.9192-35.5118
300.0684-0.0232-0.18960.06920.10230.75310.02950.1536-0.0877-0.1588-0.0291-0.32040.0053-0.02540.01390.1127-0.00450.06660.1280.03140.1869-4.674667.4312-37.2011
310.6760.09330.06830.1541-0.04370.026-0.05480.3780.0542-0.13890.1212-0.05290.04790.089-0.02750.1805-0.0029-0.00210.1984-0.01610.1118-16.966162.2094-40.2022
320.4892-0.17610.10660.070.01050.2482-0.0029-0.074-0.46880.034-0.0993-0.17330.0494-0.0131-0.0340.1242-0.005-0.04540.17890.08060.3143-6.095452.208-24.1937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resseq 158:203)B158 - 203
2X-RAY DIFFRACTION2chain 'B' and (resseq 204:213)B204 - 213
3X-RAY DIFFRACTION3chain 'B' and (resseq 214:249)B214 - 249
4X-RAY DIFFRACTION4chain 'B' and (resseq 250:291)B250 - 291
5X-RAY DIFFRACTION5chain 'A' and (resseq 159:172)A159 - 172
6X-RAY DIFFRACTION6chain 'A' and (resseq 173:183)A173 - 183
7X-RAY DIFFRACTION7chain 'A' and (resseq 184:194)A184 - 194
8X-RAY DIFFRACTION8chain 'A' and (resseq 195:203)A195 - 203
9X-RAY DIFFRACTION9chain 'A' and (resseq 204:213)A204 - 213
10X-RAY DIFFRACTION10chain 'A' and (resseq 214:222)A214 - 222
11X-RAY DIFFRACTION11chain 'A' and (resseq 223:231)A223 - 231
12X-RAY DIFFRACTION12chain 'A' and (resseq 232:239)A232 - 239
13X-RAY DIFFRACTION13chain 'A' and (resseq 240:262)A240 - 262
14X-RAY DIFFRACTION14chain 'A' and (resseq 263:271)A263 - 271
15X-RAY DIFFRACTION15chain 'A' and (resseq 272:278)A272 - 278
16X-RAY DIFFRACTION16chain 'A' and (resseq 279:290)A279 - 290
17X-RAY DIFFRACTION17chain 'C' and (resseq 160:172)C160 - 172
18X-RAY DIFFRACTION18chain 'C' and (resseq 173:222)C173 - 222
19X-RAY DIFFRACTION19chain 'C' and (resseq 223:262)C223 - 262
20X-RAY DIFFRACTION20chain 'C' and (resseq 263:289)C263 - 289
21X-RAY DIFFRACTION21chain 'D' and (resseq 160:172)D160 - 172
22X-RAY DIFFRACTION22chain 'D' and (resseq 173:194)D173 - 194
23X-RAY DIFFRACTION23chain 'D' and (resseq 195:203)D195 - 203
24X-RAY DIFFRACTION24chain 'D' and (resseq 204:213)D204 - 213
25X-RAY DIFFRACTION25chain 'D' and (resseq 214:222)D214 - 222
26X-RAY DIFFRACTION26chain 'D' and (resseq 223:231)D223 - 231
27X-RAY DIFFRACTION27chain 'D' and (resseq 232:239)D232 - 239
28X-RAY DIFFRACTION28chain 'D' and (resseq 240:249)D240 - 249
29X-RAY DIFFRACTION29chain 'D' and (resseq 250:262)D250 - 262
30X-RAY DIFFRACTION30chain 'D' and (resseq 263:271)D263 - 271
31X-RAY DIFFRACTION31chain 'D' and (resseq 272:278)D272 - 278
32X-RAY DIFFRACTION32chain 'D' and (resseq 279:288)D279 - 288

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