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- PDB-2h2t: CD23 Lectin domain, Calcium 2+-bound -

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Basic information

Entry
Database: PDB / ID: 2h2t
TitleCD23 Lectin domain, Calcium 2+-bound
ComponentsLow affinity immunoglobulin epsilon Fc receptor (Lymphocyte IgE receptor) (Fc-epsilon-RII) (Immunoglobulin E-binding factor) (CD23 antigen)
KeywordsIMMUNE SYSTEM / C-type lectin / calcium-bound / lectin domain / low affinity IgE 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: 1.3 Å
AuthorsWurzburg, B.A.
CitationJournal: Structure / Year: 2006
Title: Structural Changes in the Lectin Domain of CD23, the Low-Affinity IgE Receptor, upon Calcium Binding.
Authors: Wurzburg, B.A. / Tarchevskaya, S.S. / Jardetzky, T.S.
History
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ACCORDING TO AUTHORS, INTACT HUMAN CD23 IS THOUGHT TO FORM A TRIMER, HOWEVER, THE EXACT RELATIONSHIP OF THE LECTIN DOMAINS IN THE MULTIMER IS NOT CURRENTLY KNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Low affinity immunoglobulin epsilon Fc receptor (Lymphocyte IgE receptor) (Fc-epsilon-RII) (Immunoglobulin E-binding factor) (CD23 antigen)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5562
Polymers19,5161
Non-polymers401
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.310, 51.261, 58.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIntact human CD23 is thought to form a trimer, although it is possible that it forms a tetramer. The exact relationship of the monomer lectin domains to each other is not currently known.

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Components

#1: Protein Low affinity immunoglobulin epsilon Fc receptor (Lymphocyte IgE receptor) (Fc-epsilon-RII) (Immunoglobulin E-binding factor) (CD23 antigen)


Mass: 19515.717 Da / Num. of mol.: 1 / Fragment: lectin domain / Mutation: H213R, G256S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCER2 / Plasmid: pBACgus-3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf+ / References: UniProt: P06734
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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 % sol: 20.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 17% (w/v) PEG 4000, 100 mM Mes buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.02336 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02336 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 30523 / Num. obs: 30523 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 14.74 Å2 / Rsym value: 0.09 / Net I/σ(I): 41.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1515 / Rsym value: 0.338 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H2R

2h2r


Resolution: 1.3→38.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.37 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20045 1561 5.1 %THIN SHELLS
Rwork0.16785 ---
all0.16953 28870 --
obs0.16953 28870 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.56 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 157 1159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211058
X-RAY DIFFRACTIONr_bond_other_d0.0020.02894
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9061435
X-RAY DIFFRACTIONr_angle_other_deg2.52732085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7235128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96123.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69215173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.542159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_nbd_refined0.2360.2213
X-RAY DIFFRACTIONr_nbd_other0.2220.2951
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2501
X-RAY DIFFRACTIONr_nbtor_other0.0870.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2510.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0310.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.40.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.213
X-RAY DIFFRACTIONr_mcbond_it4.9973643
X-RAY DIFFRACTIONr_mcbond_other3.3633264
X-RAY DIFFRACTIONr_mcangle_it5.8284994
X-RAY DIFFRACTIONr_scbond_it6.0693502
X-RAY DIFFRACTIONr_scangle_it7.4734438
X-RAY DIFFRACTIONr_rigid_bond_restr3.76232315
X-RAY DIFFRACTIONr_sphericity_free18.2033155
X-RAY DIFFRACTIONr_sphericity_bonded7.931917
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 77 -
Rwork0.292 2134 -
obs-2134 100 %

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