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- PDB-4j6m: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -

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Basic information

Entry
Database: PDB / ID: 4j6m
TitleCrystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form D)
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: 2.48 Å
AuthorsDhaliwal, B. / Fabiane, S.M. / 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 ...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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,70412
Polymers129,3208
Non-polymers3844
Water4,288238
1
A: 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
2
B: 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
3
C: 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
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
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


Theoretical massNumber of molelcules
Total (without water)16,1651
Polymers16,1651
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)16,1651
Polymers16,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.289, 65.098, 106.780
Angle α, β, γ (deg.)95.260, 88.880, 89.620
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.: 238 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22.5 % (w/v) PEG 3,350, 0.2 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: I03 / Wavelength: 0.9745 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 47011 / Num. obs: 46992 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.04 / % possible all: 74.9

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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: 2.48→36.31 Å / Cor.coef. Fo:Fc: 0.8854 / Cor.coef. Fo:Fc free: 0.8483 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2376 5.06 %THIN
Rwork0.2082 ---
obs0.2099 46992 94.6 %-
all-47011 --
Displacement parametersBiso max: 120.84 Å2 / Biso mean: 31.648 Å2 / Biso min: 4.17 Å2
Baniso -1Baniso -2Baniso -3
1-10.6373 Å2-5.6882 Å21.9514 Å2
2---5.0703 Å2-6.1692 Å2
3----5.567 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.48→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8527 0 20 238 8785
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2953SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes215HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1291HARMONIC5
X-RAY DIFFRACTIONt_it8840HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1053SEMIHARMONIC5
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_contact9592SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8840HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11997HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion19.2
LS refinement shellResolution: 2.48→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3259 142 5.48 %
Rwork0.268 2450 -
all0.2714 2592 -
obs--94.6 %
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)
11.12950.26320.23191.09080.52621.96410.04740.0508-0.0034-0.0052-0.06220.04870.03840.05480.0148-0.06420.01420.0137-0.1220.0175-0.0352-23.6177-14.250116.1792
21.3751-0.32660.26281.6383-0.49231.74930.0133-0.019-0.0491-0.0788-0.04080.02990.0333-0.0330.0274-0.05850.00280.0044-0.09680.0059-0.0553-29.8485-17.983444.602
30.9819-0.7021-0.15241.35060.46482.02870.02390.10.0011-0.0136-0.032-0.0217-0.05410.07150.0081-0.0645-0.0004-0.0037-0.10060.0158-0.0332-49.9138-44.814944.5543
42.25720.1011-0.71320.90610.69012.72420.0417-0.2531-0.02880.02270.04950.03230.0310.0176-0.0911-0.07620.04520.0185-0.07160.0247-0.1017-51.2759-20.738866.918
52.44980.1656-0.1791.0588-0.09731.67960.00790.14320.0068-0.03350.0690.0868-0.0569-0.0256-0.0769-0.0819-0.0016-0.0022-0.07730.0233-0.0819-54.6736-17.5106-6.2917
60.9308-0.1882-0.19731.2453-0.36531.91080.03260.0092-0.0127-0.0053-0.05430.0452-0.0058-0.03110.0217-0.06050.00520.0013-0.09860.0036-0.0273-55.9016-41.621116.04
72.7453-0.61240.84870.8978-0.15292.44080.04780.198-0.03730.0397-0.005-0.04150.09380.0476-0.0429-0.0638-0.0035-0.005-0.09240.0174-0.0706-25.4886-37.9353-5.5458
83.77170.35690.54630.9963-0.37291.91680.0642-0.306-0.1280.02250.0415-0.0470.0474-0.0184-0.1057-0.05870.0412-0.0188-0.08510.0249-0.0803-28.0692-42.126466.186
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|* }C157 - 291
4X-RAY DIFFRACTION4{ D|* }D157 - 290
5X-RAY DIFFRACTION5{ E|* }E157 - 290
6X-RAY DIFFRACTION6{ F|* }F157 - 291
7X-RAY DIFFRACTION7{ G|* }G160 - 288
8X-RAY DIFFRACTION8{ H|* }H160 - 288

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