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- PDB-6pwt: Crystal structure of the cow C-type carbohydrate-recognition doma... -

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Basic information

Entry
Database: PDB / ID: 6pwt
TitleCrystal structure of the cow C-type carbohydrate-recognition domain of CD23 in the presence of GlcNAc2Man3 oligosaccharide
ComponentsFc fragment of IgE receptor II
KeywordsSUGAR BINDING PROTEIN / CRD / Receptor / Lectin / Metal-Binding
Function / homology
Function and homology information


signaling receptor activity / carbohydrate binding / immune response / external side of plasma membrane / metal ion binding
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
Fc epsilon receptor II
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.701 Å
AuthorsWeis, W.I. / Feinberg, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P005659/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: CD23 is a glycan-binding receptor in some mammalian species.
Authors: Jegouzo, S.A.F. / Feinberg, H. / Morrison, A.G. / Holder, A. / May, A. / Huang, Z. / Jiang, L. / Lasanajak, Y. / Smith, D.F. / Werling, D. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
History
DepositionJul 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2019Group: Data collection / 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 / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Fc fragment of IgE receptor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3404
Polymers15,3491
Non-polymers9913
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.167, 33.167, 207.814
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fc fragment of IgE receptor II


Mass: 15349.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: FCER2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1BIQ4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2-1-2/a3-b1_a6-d1_b2-c1_d2-e1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsResidue numbering based on NCBI Reference Sequence: XP_002688905.2

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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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution: 5 mg/ml protein, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, and 10 mM GlcNAc2Man3. reservoir solution: 22% polyethylene glycol 8K, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→34.64 Å / Num. obs: 4156 / % possible obs: 99.5 % / Redundancy: 16.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.027 / Rrim(I) all: 0.108 / Net I/σ(I): 13.7 / Num. measured all: 70226 / Scaling rejects: 177
Reflection shellResolution: 2.7→2.876 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.344 / Num. measured all: 6699 / Num. unique obs: 518 / CC1/2: 0.985 / Rpim(I) all: 0.1 / Rrim(I) all: 0.359 / Net I/σ(I) obs: 3.1 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PWS

6pws


Resolution: 2.701→34.636 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2509 183 4.45 %
Rwork0.1988 --
obs0.201 4109 99.18 %
Displacement parametersBiso max: 179.93 Å2 / Biso mean: 85.3 Å2 / Biso min: 39.52 Å2
Refinement stepCycle: final / Resolution: 2.701→34.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 64 1 1112
Biso mean--78.51 40.83 -
Num. residues----129
LS refinement shellResolution: 2.701→2.876 Å
RfactorNum. reflection% reflection
Rwork0.2591 638 -
Rfree-32 -
obs-670 96.13 %
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)
18.204-2.79966.32025.1362-4.46896.1495-0.08881.66190.1587-1.9970.0693-0.83880.32920.848-0.09712.4512-0.26790.07970.9285-0.2030.505717.4030.92273.2912
24.0353-0.0999-1.93150.0867-0.53557.5883-0.53530.1697-0.9634-1.13610.6674-0.32350.49651.1651-0.31581.3417-0.030.03710.4582-0.09760.473817.0241-0.2219.5054
34.7495-1.3911-1.09393.8169-0.9922.0355-0.25071.0365-0.9578-1.95480.08290.9420.45780.0806-0.19952.0078-0.3365-0.28540.3425-0.00470.50549.19153.824213.6312
46.7176-4.72950.37993.3806-0.21498.2177-0.24680.09451.0546-1.68940.26290.6693-2.07720.31030.02751.0622-0.1384-0.23210.27980.04290.73919.403715.082321.9699
56.0777-3.3407-1.17556.09474.5836.6079-0.59910.3528-0.5103-0.92660.02950.94250.6668-0.07980.4290.9172-0.1516-0.11680.35210.07580.62029.54054.684821.6524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 174 )A162 - 174
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 195 )A175 - 195
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 224 )A196 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 254 )A225 - 254
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 290 )A255 - 290

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