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- PDB-4j6q: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -

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Basic information

Entry
Database: PDB / ID: 4j6q
TitleCrystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form G)
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 / positive regulation of killing of cells of another organism / : / 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 / positive regulation of killing of cells of another organism / : / Interleukin-10 signaling / positive regulation of nitric-oxide synthase activity / integrin binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / protease binding / immune response / external side of plasma membrane / 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: 2.539 Å
AuthorsDhaliwal, B. / Pang, M.O.Y. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Low affinity immunoglobulin epsilon Fc receptor

A: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)32,3302
Polymers32,3302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 73.180, 62.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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.: 1
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.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 41.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 3.7 M NaCl and 0.1 M citric acid pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.539→37.1 Å / Num. all: 4740 / Num. obs: 4727 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.54→2.6 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
xia2data scaling
PHASESphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G96

4g96


Resolution: 2.539→31.625 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.23 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1226 14.13 %RANDOM
Rwork0.1689 ---
obs0.1789 8675 99.63 %-
all-8675 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.142 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 116.65 Å2 / Biso mean: 33.0487 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.1225 Å2-0 Å20 Å2
2---4.8826 Å2-0 Å2
3---7.0051 Å2
Refinement stepCycle: LAST / Resolution: 2.539→31.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 0 35 1099
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)
12.02880.4569-0.26421.6627-0.99623.6956-0.0173-0.0402-0.2971-0.19210.03390.08690.5029-0.34550.20670.1202-0.0245-0.02250.12010.01860.308411.63910.8388-10.8501
22.4099-0.2679-0.19044.11311.60862.775-0.00190.02390.20520.0859-0.110.5148-0.2156-0.2125-0.07340.06610.01560.05050.0954-0.01040.05114.899314.1671-4.9476
31.66680.53020.15362.10550.32461.76120.1148-0.27820.03910.0261-0.09220.41610.0916-0.21030.13540.0846-0.02320.00340.0605-0.0320.171417.030110.75421.6938
42.73810.146-1.02613.152-0.61182.8716-0.09630.2576-0.2649-0.26690.0661-0.16310.0965-0.13520.09950.0331-0.00090.07490.1706-0.04350.090724.41267.7509-13.5845
50.19740.41170.05481.19280.73921.1271-0.07090.29940.4002-0.2602-0.12910.2066-0.3244-0.2936-0.2327-0.00330.1395-0.12560.23770.13450.249821.078517.8189-7.5002
68.2240.25120.56595.4686-2.06874.2872-0.1269-1.5389-0.30251.30530.1752-0.90810.33390.6604-0.07610.29460.1274-0.16390.3196-0.0310.247831.002210.42779.3871
73.6611.6555-0.52295.12790.62944.03150.2608-0.2205-0.49120.2683-0.1373-0.31840.22320.092-0.1380.1266-0.1051-0.15510.0552-0.05910.31328.72835.93363.6476
82.1194-0.5611-0.34250.1632-0.06891.7853-0.02230.03380.12310.0057-0.1055-0.1495-0.03040.1879-0.4270.0047-0.09240.00750.12820.00360.324434.348611.5198-5.5229
96.3885-1.2222-0.69434.2063-0.610.2482-0.0151-1.10640.54110.51580.1615-0.4315-0.15890.1658-0.2380.0991-0.03820.04120.23-0.11160.259331.71417.54073.5356
103.64530.30590.57472.18831.00823.181-0.08770.07030.5107-0.06970.0025-0.115-0.27850.0176-0.16420.00780.0026-0.01530.06750.00950.165729.969818.348-5.1372
113.23150.33011.87242.0623-0.271.9455-0.19980.09970.2469-0.10950.0814-0.2074-0.23510.1432-0.24070.1197-0.05940.10770.00980.05380.334722.224824.07021.8557
123.3435-0.2679-0.97275.7581-1.11.1764-0.04220.1465-0.3958-0.13160.21930.23120.145-0.13190.346-0.00150.02920.09450.09830.01090.001613.26284.6612-5.3595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 158:172)A158 - 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 204:212)A204 - 212
5X-RAY DIFFRACTION5chain 'A' and (resseq 213:222)A213 - 222
6X-RAY DIFFRACTION6chain 'A' and (resseq 223:230)A223 - 230
7X-RAY DIFFRACTION7chain 'A' and (resseq 231:239)A231 - 239
8X-RAY DIFFRACTION8chain 'A' and (resseq 240:249)A240 - 249
9X-RAY DIFFRACTION9chain 'A' and (resseq 250:262)A250 - 262
10X-RAY DIFFRACTION10chain 'A' and (resseq 263:272)A263 - 272
11X-RAY DIFFRACTION11chain 'A' and (resseq 273:278)A273 - 278
12X-RAY DIFFRACTION12chain 'A' and (resseq 279:289)A279 - 289

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