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- PDB-6y0l: Crystal structure of human CD23 lectin domain N225D, K229E, S252N... -

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Basic information

Entry
Database: PDB / ID: 6y0l
TitleCrystal structure of human CD23 lectin domain N225D, K229E, S252N, T251N, R253G, S254G mutant
ComponentsLow affinity immunoglobulin epsilon Fc receptor membrane-bound form
KeywordsIMMUNE SYSTEM / Antibody receptor / C-type lectin / calcium binding protein / IgE / immunoglobulin E / CD23
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. / 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
Similarity search - Domain/homology
Low affinity immunoglobulin epsilon Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsIlkow, V.F. / Davies, A.M. / Sutton, B.J. / McDonnell, J.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
Wellcome Trust085944 United Kingdom
CitationJournal: Febs Open Bio / Year: 2021
Title: Reviving lost binding sites: Exploring calcium-binding site transitions between human and murine CD23.
Authors: Ilkow, V.F. / Davies, A.M. / Dhaliwal, B. / Beavil, A.J. / Sutton, B.J. / McDonnell, J.M.
History
DepositionFeb 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 23, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.seq_num / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jul 7, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 2.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.3Jan 24, 2024Group: 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

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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 membrane-bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4485
Polymers16,0761
Non-polymers3724
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-12 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.704, 113.704, 45.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-186-

HIS

21A-519-

HOH

31A-524-

HOH

41A-565-

HOH

51A-586-

HOH

61A-594-

HOH

71A-620-

HOH

81A-625-

HOH

91A-628-

HOH

101A-642-

HOH

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Components

#1: Protein Low affinity immunoglobulin epsilon Fc receptor membrane-bound form


Mass: 16075.762 Da / Num. of mol.: 1 / Mutation: N225D, K229E, S252N, T251N, R253G, S254G
Source method: isolated from a genetically manipulated source
Details: Mutations: N225D, K229E, S252N, T251N, R253G, S254G
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0M ammonium sulphate, 0.2M sodium chloride, 0.1M sodium-cacodylate, 8mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.65→98.48 Å / Num. obs: 20443 / % possible obs: 94.36 % / Redundancy: 11.5 % / Biso Wilson estimate: 19.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Net I/σ(I): 16.6
Reflection shellResolution: 1.65→1.73 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.58 / Rpim(I) all: 0.413 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G9A

4g9a


Resolution: 1.65→56.852 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2051 1016 5.01 %
Rwork0.1667 --
obs0.1686 20266 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→56.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 23 152 1221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121174
X-RAY DIFFRACTIONf_angle_d1.2461609
X-RAY DIFFRACTIONf_dihedral_angle_d15.812690
X-RAY DIFFRACTIONf_chiral_restr0.072156
X-RAY DIFFRACTIONf_plane_restr0.008206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6502-1.73720.29111480.21992807X-RAY DIFFRACTION98
1.7372-1.84610.23021490.1822839X-RAY DIFFRACTION100
1.8461-1.98860.26941190.19882263X-RAY DIFFRACTION79
1.9886-2.18880.21121460.14452770X-RAY DIFFRACTION96
2.1888-2.50550.20241420.16322683X-RAY DIFFRACTION93
2.5055-3.15660.21231520.17042880X-RAY DIFFRACTION98
3.1566-56.88570.17621600.15753008X-RAY DIFFRACTION96

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