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- PDB-4j6p: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -

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Basic information

Entry
Database: PDB / ID: 4j6p
TitleCrystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form F)
ComponentsLow affinity immunoglobulin epsilon Fc receptor
KeywordsIMMUNE SYSTEM / immunoglobulin fold lectin / antibody 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: 1.9 Å
AuthorsDhaliwal, B. / Yuan, D. / Sutton, B.J.
CitationJournal: Mol.Immunol. / Year: 2013
Title: Conformational plasticity at the IgE-binding site of the B-cell receptor CD23.
Authors: Dhaliwal, B. / Pang, M.O. / Yuan, D. / Yahya, N. / Fabiane, S.M. / McDonnell, J.M. / Gould, H.J. / Beavil, A.J. / Sutton, B.J.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)64,6604
Polymers64,6604
Non-polymers00
Water4,954275
1
A: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.670, 89.920, 101.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Soluble head domain of the B-cell receptor CD23 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: 22.5 % (w/v) PEG 4,000 and 0.1 M sodium citrate pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→45.8 Å / Num. all: 45855 / Num. obs: 45754 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.23 Å2
Reflection shellResolution: 1.9→2 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
xia2data scaling
PHASESphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G96

4g96


Resolution: 1.9→27.82 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9395 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 2311 5.05 %RANDOM
Rwork0.1858 ---
obs0.1873 45754 99.93 %-
all-45855 --
Displacement parametersBiso mean: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.5275 Å20 Å20 Å2
2--1.4843 Å20 Å2
3----5.0118 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 0 275 4501
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014391HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.115955HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1485SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes650HARMONIC5
X-RAY DIFFRACTIONt_it4391HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion17.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion525SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5118SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2798 142 4.28 %
Rwork0.252 3175 -
all0.2532 3317 -
obs--99.93 %
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)
12.57670.6918-0.15363.01190.31160.6250.0067-0.04490.0542-0.16010.0180.0142-0.10250.0316-0.02470.0808-0.0749-0.002-0.16760.02130.1391-12.704721.25881.2165
21.90830.8622-1.0024.3731-0.53881.7021-0.02290.04240.19-0.13440.019-0.1887-0.1680.08220.0038-0.041-0.0503-0.0279-0.14860.00770.0329-13.75597.09173.5797
30.9751.45352.283800.91600.0043-0.04470.06-0.117-0.0348-0.1684-0.06760.05260.0305-0.1085-0.12860.0195-0.1496-0.01060.3016-0.748915.1026-0.2036
41.55571.7776-1.374700.16050.5515-0.0122-0.02070.0910.10460.0059-0.2299-0.05530.07440.0063-0.0361-0.0062-0.0509-0.0843-0.04610.1586-4.28624.88335.8162
53.5563-2.5786-0.70521.34742.87751.4784-0.01570.263-0.1303-0.3175-0.0032-0.25970.0316-0.01430.01890.0736-0.030.0777-0.109-0.00840.0352-8.3671-0.291-8.7878
61.9943-0.74110.12161.23080.70330.00050.0256-0.0132-0.0225-0.0358-0.0066-0.13490.13450.1966-0.019-0.16730.01890.0907-0.1954-0.05580.30251.1513-2.8876-2.7671
72.15240.28410.55574.37190.19171.8711-0.0034-0.06120.0915-0.0301-0.0073-0.5442-0.0850.37670.0107-0.1314-0.04390.0026-0.12060.02110.1292-5.46212.52713.7452
80.32691.19292.20120.55970.234500.01540.0826-0.0131-0.0010.0026-0.0411-0.0268-0.0594-0.01790.1458-0.0439-0.1519-0.21260.15140.1453-18.849128.0523-6.5466
93.8575-0.294-1.10571.1736-2.01333.90830.01180.20290.1045-0.17190.02890.0121-0.04980.1465-0.04060.11350.01710.004-0.14760.0078-0.0084-24.771615.5952-22.0576
101.5485-0.1338-0.50563.64940.10971.1666-0.09490.062-0.0139-0.28080.08780.07270.0649-0.10030.00710.0470.0239-0.0256-0.1290.01030.0046-31.89374.4596-13.2417
111.8239-0.17860.20790.0002-0.61720.02440.00840.12790.0834-0.02590.03780.0246-0.1478-0.0299-0.04610.12960.0854-0.0867-0.0840.05770.0214-39.108717.4373-18.9488
121.0602-0.6134-0.210.91331.14592.0537-0.05750.0331-0.1252-0.0295-0.01320.15290.0532-0.04160.07080.04940.0399-0.0975-0.0696-0.0410.1278-41.57465.9875-17.2664
130.2043-2.00911.502300.53580.1607-0.0156-0.05160.04-0.00180.03080.16440.0160.0165-0.01530.03390.06260.1023-0.029-0.01190.0347-39.25418.20362.8269
143.9559-1.2986-0.79673.6751-1.00792.6193-0.0534-0.01750.17270.09890.06920.527-0.1664-0.3761-0.0159-0.07310.0538-0.0139-0.1333-0.00720.0672-42.13211.4236-4.7597
150-0.2179-0.16981.42040.71780-0.00250.0750.1221-0.0637-0.01730.08810.0734-0.15780.0197-0.01580.0756-0.1151-0.0393-0.03030.1461-46.842810.05-11.611
162.3975-0.67161.87970.5002-0.30270.6223-0.0044-0.0482-0.0223-0.04990.01430.08970.0367-0.0961-0.00990.0289-0.0170.0184-0.1034-0.04660.2218-43.5837-2.8452-9.167
170.7331-0.3415-0.1780.82920.98252.150.04040.0487-0.0732-0.1140.1357-0.011-0.20260.2465-0.17610.09760.03060.015-0.12830.0324-0.0452-25.653311.3113-17.6987
183.64191.06430.13320.1380.10372.009-0.022-0.1987-0.02140.04180.1182-0.0546-0.01710.0427-0.09620.03010.0102-0.07120.11410.0875-0.0806-22.229-10.374630.3776
192.7329-0.05210.57342.1135-2.91043.8923-0.0257-0.31590.07310.239-0.0954-0.266-0.0890.12270.1211-0.0094-0.0409-0.0055-0.07580.02450.0179-23.445-2.033715.0228
201.74882.7051.07290.2878-2.10672.9844-0.0571-0.3896-0.13940.3386-0.00410.0869-0.0762-0.24240.06120.0168-0.01480.02660.03050.0797-0.0808-32.2417-8.197723.1216
216.0914-0.52630.09392.2948-1.38495.19360.0895-0.1844-0.2132-0.08730.03090.29240.2467-0.5442-0.1204-0.0831-0.0159-0.0376-0.05720.0463-0.0207-35.9228-8.977911.5495
223.481.5262.45830.5934-2.88980-0.0698-0.09080.0999-0.24690.19460.2655-0.0294-0.2246-0.1247-0.02110.01240.0266-0.07080.02930.0268-38.8543-3.35358.7582
231.1459-0.04750.70330.8280.34561.47450.048-0.42440.01110.1953-0.08960.01430.1541-0.02740.04160.0154-0.0337-0.00870.00650.0480.004-23.821-6.095520.59
244.0457-1.38272.24.01970.57970-0.03550.2039-0.28960.0196-0.00030.1062-0.02740.05070.03580.047-0.08240.0664-0.1962-0.05180.0333-36.8438-28.256-16.4557
252.96991.09640.87154.141.16152.7181-0.14570.1865-0.3917-0.17780.2438-0.38450.19430.0283-0.09810.038-0.02160.067-0.1505-0.03280.0362-27.0332-18.6823-11.8606
260.0008-1.0553-0.14640.94862.58190.3654-0.0034-0.2597-0.06330.05940.0182-0.00740.15660.0647-0.01490.0957-0.0076-0.0242-0.10060.03280.0193-24.4896-17.36073.5782
272.5231.21861.52010.38181.52282.25430.0167-0.1376-0.25970.0680.0567-0.38110.12140.0884-0.0734-0.01990.0301-0.0032-0.25010.02570.1763-16.7746-18.7736-0.8629
280.0002-0.84842.02510.4547-2.91040.0634-0.01040.1152-0.31810.0226-0.0285-0.1161-0.02770.17480.0389-0.02850.03530.0811-0.2103-0.06360.1977-15.1576-19.1866-7.1446
291.66611.12742.09121.59621.63531.0546-0.035-0.0402-0.1035-0.00430.0194-0.03640.0286-0.040.01560.1225-0.02650.0633-0.1088-0.02620.0765-28.5245-16.0111-12.0686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|160 - 172}A160 - 172
2X-RAY DIFFRACTION2{A|173 - 203}A173 - 203
3X-RAY DIFFRACTION3{A|204 - 213}A204 - 213
4X-RAY DIFFRACTION4{A|214 - 223}A214 - 223
5X-RAY DIFFRACTION5{A|224 - 243}A224 - 243
6X-RAY DIFFRACTION6{A|244 - 258}A244 - 258
7X-RAY DIFFRACTION7{A|259 - 285}A259 - 285
8X-RAY DIFFRACTION8{A|286 - 291}A286 - 291
9X-RAY DIFFRACTION9{B|158 - 172}B158 - 172
10X-RAY DIFFRACTION10{B|173 - 203}B173 - 203
11X-RAY DIFFRACTION11{B|204 - 212}B204 - 212
12X-RAY DIFFRACTION12{B|213 - 222}B213 - 222
13X-RAY DIFFRACTION13{B|223 - 231}B223 - 231
14X-RAY DIFFRACTION14{B|232 - 262}B232 - 262
15X-RAY DIFFRACTION15{B|263 - 271}B263 - 271
16X-RAY DIFFRACTION16{B|272 - 278}B272 - 278
17X-RAY DIFFRACTION17{B|279 - 290}B279 - 290
18X-RAY DIFFRACTION18{C|158 - 172}C158 - 172
19X-RAY DIFFRACTION19{C|173 - 194}C173 - 194
20X-RAY DIFFRACTION20{C|195 - 213}C195 - 213
21X-RAY DIFFRACTION21{C|214 - 249}C214 - 249
22X-RAY DIFFRACTION22{C|250 - 272}C250 - 272
23X-RAY DIFFRACTION23{C|273 - 292}C273 - 292
24X-RAY DIFFRACTION24{D|157 - 172}D157 - 172
25X-RAY DIFFRACTION25{D|173 - 222}D173 - 222
26X-RAY DIFFRACTION26{D|223 - 239}D223 - 239
27X-RAY DIFFRACTION27{D|240 - 262}D240 - 262
28X-RAY DIFFRACTION28{D|263 - 272}D263 - 272
29X-RAY DIFFRACTION29{D|273 - 288}D273 - 288

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