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- PDB-4gjx: Crystal structure of CD23 lectin domain mutant D258A -

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Basic information

Entry
Database: PDB / ID: 4gjx
TitleCrystal structure of CD23 lectin domain mutant D258A
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 / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / 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 / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling / positive regulation of nitric-oxide synthase activity / integrin binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / 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) / C-type lectin-like/link domain superfamily ...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: 2.8 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 10, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: Low affinity immunoglobulin epsilon Fc receptor
F: Low affinity immunoglobulin epsilon Fc receptor
G: Low affinity immunoglobulin epsilon Fc receptor
H: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,15210
Polymers128,9688
Non-polymers1842
Water2,936163
1
A: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2132
Polymers16,1211
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1211
Polymers16,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1211
Polymers16,1211
Non-polymers00
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)16,2132
Polymers16,1211
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1211
Polymers16,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1211
Polymers16,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1211
Polymers16,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1211
Polymers16,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.970, 90.970, 351.681
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSARGARGAA160 - 2245 - 69
21CYSCYSARGARGBB160 - 2245 - 69
31CYSCYSARGARGCC160 - 2245 - 69
41CYSCYSARGARGDD160 - 2245 - 69
51CYSCYSARGARGEE160 - 2245 - 69
61CYSCYSARGARGFF160 - 2245 - 69
71CYSCYSARGARGGG160 - 2245 - 69
81CYSCYSARGARGHH160 - 2245 - 69
12PHEPHEPROPROAA232 - 25077 - 95
22PHEPHEPROPROBB232 - 25077 - 95
32PHEPHEPROPROCC232 - 25077 - 95
42PHEPHEPROPRODD232 - 25077 - 95
52PHEPHEPROPROEE232 - 25077 - 95
62PHEPHEPROPROFF232 - 25077 - 95
72PHEPHEPROPROGG232 - 25077 - 95
82PHEPHEPROPROHH232 - 25077 - 95
13CYSCYSCYSCYSAA259 - 288104 - 133
23CYSCYSCYSCYSBB259 - 288104 - 133
33CYSCYSCYSCYSCC259 - 288104 - 133
43CYSCYSCYSCYSDD259 - 288104 - 133
53CYSCYSCYSCYSEE259 - 288104 - 133
63CYSCYSCYSCYSFF259 - 288104 - 133
73CYSCYSCYSCYSGG259 - 288104 - 133
83CYSCYSCYSCYSHH259 - 288104 - 133

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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: 16120.977 Da / Num. of mol.: 8 / Fragment: UNP residues 156-298 / Mutation: D258A
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, 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 315 / Detector: CCD / Date: Jan 21, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→58.67 Å / Num. all: 40357 / Num. obs: 36967 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.95 Å / % possible all: 94.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H2R

2h2r


Resolution: 2.8→58.67 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.46 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1834 5 %RANDOM
Rwork0.2077 ---
all0.2099 40357 --
obs0.2099 36868 91.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.59 Å2 / Biso mean: 50.6608 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.8→58.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8630 0 12 163 8805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.028950
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.90312150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42551072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69623.214448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.633151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4751564
X-RAY DIFFRACTIONr_chiral_restr0.070.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217020
Refine LS restraints NCS

Ens-ID: 1 / Number: 920 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.270.5
2BMEDIUM POSITIONAL0.260.5
3CMEDIUM POSITIONAL0.240.5
4DMEDIUM POSITIONAL0.290.5
5EMEDIUM POSITIONAL0.290.5
6FMEDIUM POSITIONAL0.280.5
7GMEDIUM POSITIONAL0.260.5
8HMEDIUM POSITIONAL0.240.5
1AMEDIUM THERMAL7.312
2BMEDIUM THERMAL3.732
3CMEDIUM THERMAL10.612
4DMEDIUM THERMAL2.362
5EMEDIUM THERMAL2.492
6FMEDIUM THERMAL7.212
7GMEDIUM THERMAL3.912
8HMEDIUM THERMAL11.722
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 134 -
Rwork0.28 2667 -
all-2801 -
obs--94.5 %
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)
12.18710.51520.88050.80420.73373.36170.0551-0.3708-0.0181-0.1746-0.02330.0810.0193-0.0459-0.03180.1421-0.0375-0.01550.1862-0.02090.2362-33.3727-2.23443.4977
20.980.18080.02522.22521.36862.96820.2525-0.18320.0284-0.0008-0.2458-0.0170.1549-0.1722-0.00670.1295-0.13890.04650.2357-0.09060.2198-62.549-3.8213-8.1439
31.79931.1094-0.34022.75612.02022.63410.5337-0.52060.00820.5126-0.5235-0.02690.27930.0363-0.01020.4805-0.07760.06160.33790.02570.0296-17.102922.6682-8.2195
41.5571-0.7468-1.59722.05390.81752.98850.06470.00560.0089-0.29560.02180.06940.0336-0.1123-0.08650.3277-0.05620.00270.066-0.00890.1846-33.5338-1.4011-30.5411
52.2827-0.3532-1.64651.97570.94632.32720.1809-0.3203-0.13780.072-0.14380.00060.07070.1725-0.03720.1774-0.12630.01940.25120.01170.1538-29.923449.0252-19.8333
61.35670.7883-0.74881.214-0.55032.7643-0.19590.02560.0034-0.11680.2245-0.0010.0248-0.1181-0.02860.1487-0.02820.01640.1833-0.00860.2611-18.6258-27.76894.7167
71.59840.7248-1.3441.6469-0.31182.5943-0.1313-0.12150.024-0.31730.05920.05010.27870.00460.07210.3409-0.00390.10970.0350.02420.2277-17.576422.7215-42.2316
81.69661.2417-1.63873.7062-0.61421.7699-0.2196-0.0332-0.0021-0.97930.18690.13240.0269-0.04690.03280.4791-0.1244-0.02740.2802-0.02830.0124-62.7542-3.4823-42.1551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A158 - 292
2X-RAY DIFFRACTION2B158 - 292
3X-RAY DIFFRACTION3C158 - 291
4X-RAY DIFFRACTION4D158 - 292
5X-RAY DIFFRACTION5E158 - 292
6X-RAY DIFFRACTION6F158 - 292
7X-RAY DIFFRACTION7G158 - 292
8X-RAY DIFFRACTION8H158 - 291

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