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

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Basic information

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


pattern recognition 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) ...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
methyl alpha-D-mannopyranoside / Fc epsilon receptor II
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 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
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fc fragment of IgE receptor II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6234
Polymers15,3491
Non-polymers2743
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.553, 45.915, 69.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 (domestic cattle) / Gene: FCER2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1BIQ4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY
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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: protein solution: 4.2 mg/ml protein, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, and 50 mM alpha-methyl mannoside. reservoir solution: 16% polyethylene glycol 4K, 0.1 MES, pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.8157 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8157 Å / Relative weight: 1
ReflectionResolution: 1→38.55 Å / Num. obs: 67049 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 33.5 / Num. measured all: 429513 / Scaling rejects: 244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1-1.025.80.1191891432390.990.0540.13112.398.5
5.48-38.556.20.03430444920.9890.0160.03857.599.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H2T

2h2t


Resolution: 1→29.525 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1276 3350 5 %
Rwork0.1148 --
obs0.1154 66977 99.67 %
Displacement parametersBiso max: 52.11 Å2 / Biso mean: 10.2 Å2 / Biso min: 3.61 Å2
Refinement stepCycle: final / Resolution: 1→29.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 56 244 1347
Biso mean--16.3 20.81 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1-1.0140.1471360.1159257298
1.014-1.02920.11441370.09322615100
1.0292-1.04520.10491380.08972619100
1.0452-1.06240.09341370.08512595100
1.0624-1.08070.11011370.0886262799
1.0807-1.10040.10591380.0858261099
1.1004-1.12150.09261380.08742609100
1.1215-1.14440.10741390.08652638100
1.1444-1.16930.09541380.08562640100
1.1693-1.19650.10291390.08812623100
1.1965-1.22640.11551380.09292625100
1.2264-1.25960.09951370.0977263199
1.2596-1.29670.12531390.09992622100
1.2967-1.33850.11651380.10412645100
1.3385-1.38630.12081410.10342668100
1.3863-1.44180.1221390.10372634100
1.4418-1.50750.10371400.10052651100
1.5075-1.58690.12171390.1041265399
1.5869-1.68640.11051410.11282673100
1.6864-1.81650.11791400.11942682100
1.8165-1.99930.13181420.12892690100
1.9993-2.28850.15961420.12572705100
2.2885-2.88290.16331450.14262741100
2.8829-29.5250.14221520.13682859100

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