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- PDB-4j6j: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -

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Basic information

Entry
Database: PDB / ID: 4j6j
TitleCrystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form A)
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 / Resolution: 1.9 Å
AuthorsDhaliwal, B. / Yahya, N. / 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 1.3Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8526
Polymers64,6604
Non-polymers1922
Water3,621201
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
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
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)52.691, 56.863, 62.487
Angle α, β, γ (deg.)68.45, 87.83, 73.56
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.: 4
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 16 % (w/v) PEG 6,000, 2 % (v/v) 1,6-hexanediol, 0.05 M ammonium sulfate and 0.1 M sodium acetate pH 4.7 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→57.96 Å / Num. all: 50712 / Num. obs: 48544 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 27 / Limit h min: -27 / Limit k max: 29 / Limit k min: -27 / Limit l max: 32 / Limit l min: 0
Reflection shell% possible obs: 96.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.73 / % possible all: 96.3

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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: 1.9→15.57 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9344 / Occupancy max: 1 / Occupancy min: 0.25 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 2465 5.08 %RANDOM
Rwork0.1899 ---
obs0.1913 48510 95.56 %-
all-48564 --
Displacement parametersBiso max: 224.75 Å2 / Biso mean: 40.9941 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1-3.5138 Å21.7043 Å2-1.256 Å2
2--3.1647 Å2-1.9465 Å2
3----6.6785 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 1.9→15.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 10 201 4539
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1502SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes660HARMONIC5
X-RAY DIFFRACTIONt_it4481HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion533SEMIHARMONIC5
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_contact5089SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4481HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6076HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion16.55
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2475 151 4.57 %
Rwork0.2042 3152 -
all0.2061 3303 -
obs--95.56 %
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)
11.69420.3597-0.04851.758-0.3883.83160.221-0.07280.06620.1505-0.04760.0877-0.09490.0367-0.1734-0.0633-0.0210.0231-0.0732-0.025-0.0723-24.6225-19.046-6.3523
21.8839-0.0580.11352.83410.81461.98580.13590.1341-0.0713-0.156-0.0379-0.16470.0301-0.0235-0.098-0.08030.0174-0.0075-0.0628-0.0189-0.0537-5.0541-28.7479-30.5681
34.59760.4092-1.72224.78290.06242.45550.40370.15020.53040.018-0.29650.0379-0.4009-0.2486-0.1072-0.14490.03380.0295-0.18950.0058-0.0456-2.75821.391-16.9533
43.460.6636-1.30083.1383-1.35642.8190.18040.14850.3227-0.19970.09550.4125-0.2280.149-0.2759-0.1027-0.0027-0.0191-0.08470.0442-0.0892-26.9565-6.4608-37.0383
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 - 291

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