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- PDB-4j6l: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -

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Basic information

Entry
Database: PDB / ID: 4j6l
TitleCrystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form C)
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 / molecular replacement / Resolution: 3.15 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 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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 1.3Nov 20, 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
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


Theoretical massNumber of molelcules
Total (without water)129,3208
Polymers129,3208
Non-polymers00
Water724
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
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


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Low affinity immunoglobulin epsilon Fc receptor


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.260, 64.330, 112.200
Angle α, β, γ (deg.)75.280, 82.390, 89.950
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % (w/v) PEG 4,000, 0.15 M ammonium sulfate and 0.1 M MES pH 5.5, 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: Feb 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 23393 / Num. obs: 23393 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4g96


Resolution: 3.15→49.36 Å / Cor.coef. Fo:Fc: 0.8748 / Cor.coef. Fo:Fc free: 0.8238 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 1193 5.1 %THIN
Rwork0.2117 ---
obs0.2138 23393 96.51 %-
all-23393 --
Displacement parametersBiso max: 143.61 Å2 / Biso mean: 55.6125 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-5.059 Å2-0.9577 Å2-1.0757 Å2
2--1.6532 Å2-2.7846 Å2
3----6.7122 Å2
Refine analyzeLuzzati coordinate error obs: 0.622 Å
Refinement stepCycle: LAST / Resolution: 3.15→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 0 4 8461
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2921SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes215HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1276HARMONIC5
X-RAY DIFFRACTIONt_it8725HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1043SEMIHARMONIC5
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_contact9357SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8725HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg11819HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion20.97
LS refinement shellResolution: 3.15→3.29 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2726 114 4.61 %
Rwork0.2157 2360 -
all0.2183 2474 -
obs--96.51 %
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)
12.411-0.05750.5852.8322-1.0282.64810.0533-0.12090.0673-0.0258-0.07030.0210.0813-0.14360.017-0.15880.004-0.105-0.2312-0.08980.081922.4575-14.151-17.6981
22.4130.0212-0.37692.1702-0.23622.02390.03920.1299-0.06440.0513-0.0530.03250.04420.05760.0138-0.14760.0066-0.0906-0.243-0.03350.107128.3035-10.389-46.0661
32.6138-0.211-0.69233.68121.2762.86490.0514-0.0906-0.0190.0085-0.0387-0.0249-0.00540.1033-0.0127-0.1980.019-0.0705-0.2466-0.02370.10332.1448-41.5796-17.4814
41.2977-0.26850.64832.35810.73681.85880.01760.0719-0.0507-0.06240.081-0.07530.0794-0.0712-0.0987-0.1288-0.0267-0.0814-0.152-0.1180.061126.7565-34.9122-68.4991
51.7083-1.24730.56353.08710.05842.66480.04010.1940.01790.1091-0.04370.0541-0.0152-0.01330.0037-0.1846-0.0474-0.0465-0.2421-0.06590.1367-3.4917-37.8272-46.4913
61.5026-2.1969-0.69341.7378-0.64531.0071-0.01380.13550.053-0.02860.06080.05530.0044-0.0062-0.047-0.0901-0.0862-0.107-0.10520.02280.0798-1.3902-12.9738-67.9559
71.54970.3350.18480.5994-0.77982.5794-0.0066-0.053-0.0610.03580.07550.01250.02950.0337-0.0689-0.12690.0176-0.0558-0.16840.01750.109423.9093-38.43295.0144
81.16681.73050.03532.09631.11351.45040.0057-0.17190.0494-0.0310.0491-0.1011-0.01260.0447-0.0548-0.12220.0538-0.0958-0.087-0.09410.0618-0.1366-16.6023.9768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A157 - 291
2X-RAY DIFFRACTION2{ B|* }B157 - 291
3X-RAY DIFFRACTION3{ C|* }C158 - 291
4X-RAY DIFFRACTION4{ D|* }D158 - 290
5X-RAY DIFFRACTION5{ E|* }E159 - 291
6X-RAY DIFFRACTION6{ F|* }F160 - 288
7X-RAY DIFFRACTION7{ G|* }G157 - 291
8X-RAY DIFFRACTION8{ H|* }H160 - 288

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