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- PDB-4j6k: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -

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Basic information

Entry
Database: PDB / ID: 4j6k
TitleCrystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form B)
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 / 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 / protease 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) ...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 / molecular replacement / Resolution: 2.3 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

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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
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)129,70412
Polymers129,3208
Non-polymers3844
Water2,288127
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
MethodPISA
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
MethodPISA
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
MethodPISA
4
D: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2612
Polymers16,1651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2612
Polymers16,1651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2612
Polymers16,1651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Low affinity immunoglobulin epsilon Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2612
Polymers16,1651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.560, 56.130, 108.520
Angle α, β, γ (deg.)79.790, 84.850, 70.220
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.: 8
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: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 18 % (w/v) PEG 6,000, 2 % (v/v) 1,6-hexanediol, 0.05 M ammonium sulfate and 0.1 M sodium acetate 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: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→106.7 Å / Num. all: 47094 / Num. obs: 47059 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellRedundancy: 3.9 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3 / % possible all: 93.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9195 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.353 / Cross valid method: THIN SHELLS / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 2390 5.08 %RANDOM
Rwork0.1913 ---
obs0.1927 47059 92.24 %-
all-47094 --
Displacement parametersBiso max: 215.04 Å2 / Biso mean: 52.8599 Å2 / Biso min: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1-6.7418 Å20.9738 Å2-2.2644 Å2
2---1.8236 Å20.4669 Å2
3----4.9182 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8219 0 20 127 8366
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2856SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes211HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1238HARMONIC5
X-RAY DIFFRACTIONt_it8481HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1002SEMIHARMONIC5
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_contact9013SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8481HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11470HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion18.05
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2253 165 4.66 %
Rwork0.2079 3374 -
all0.2087 3539 -
obs--92.24 %
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)
11.89230.137-0.90991.86040.03523.29820.2312-0.25960.1080.1757-0.05530.0606-0.11610.0949-0.1758-0.083-0.0099-0.0326-0.0743-0.051-0.006525.422117.1767-9.5658
23.1404-0.3785-0.67195.7566-0.66673.52060.1550.15660.5013-0.4875-0.0698-0.0691-0.25290.1077-0.0851-0.080.0346-0.0181-0.17960.0294-0.03444.588621.0583-35.0107
33.15830.43570.9143.2408-0.29746.92180.2027-0.21870.44980.31440.16020.2767-0.4567-0.5034-0.3629-0.19480.00650.0791-0.0159-0.0314-0.098431.633232.3646-61.69
44.34790.57840.11173.75190.33611.63870.0638-0.1979-0.51420.2606-0.0783-0.06390.15610.12410.0145-0.10130.0027-0.0073-0.16770.01270.015122.314348.9592-15.3169
52.85360.4677-1.63645.5688-2.94474.33710.4060.13690.46690.2879-0.314-0.1429-0.40330.3065-0.092-0.2821-0.05040.02730.08280.1519-0.0711.68143.084-83.7933
64.4338-0.72320.09474.48360.05562.6720.1660.0239-0.22010.1138-0.5539-0.02750.5770.53580.3878-0.07370.08990.020.06320.0953-0.24338.729213.0913-71.1757
74.7141-1.23410.41194.07580.43471.93230.08110.1971-0.2219-0.399-0.08890.00140.184-0.22680.0078-0.05020.00630.0146-0.1549-0.028-0.091727.36-0.0299-36.451
85.24871.18330.95533.41131.22924.17010.12120.33980.0102-0.36120.35070.24440.5412-0.305-0.4719-0.0533-0.0764-0.1235-0.07570.0975-0.133934.899522.7372-91.1406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A159 - 288
2X-RAY DIFFRACTION2{ B|* }B162 - 286
3X-RAY DIFFRACTION3{ C|* }C162 - 287
4X-RAY DIFFRACTION4{ D|* }D156 - 288
5X-RAY DIFFRACTION5{ E|* }E158 - 289
6X-RAY DIFFRACTION6{ F|* }F159 - 287
7X-RAY DIFFRACTION7{ G|* }G157 - 287
8X-RAY DIFFRACTION8{ H|* }H163 - 290

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