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

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Basic information

Entry
Database: PDB / ID: 6pwr
TitleCrystal structure of the cow C-type carbohydrate-recognition domain of CD23 in the presence of GlcNAc-beta1-2-Man
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 / FOURIER SYNTHESIS / Resolution: 1.2 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 / struct_site / struct_site_gen
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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)15,8134
Polymers15,3491
Non-polymers4643
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.410, 45.714, 69.105
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 (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


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][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.: 221 / 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 295 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 50 mM GlcNAc-beta1-2Man. reservoir solution: 24% polyethylene glycol 8K, 0.1 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: Jan 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→38.13 Å / Num. obs: 37766 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 16.9 / Num. measured all: 236463 / Scaling rejects: 533
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
1.2-1.225.60.1521016218150.9770.070.1689.598.9
6.57-38.135.90.08516802830.960.040.09521.799.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.2→32.899 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1652 1863 5.02 %
Rwork0.1511 --
obs0.1518 37677 99.65 %
Displacement parametersBiso max: 41.48 Å2 / Biso mean: 10.1186 Å2 / Biso min: 3.04 Å2
Refinement stepCycle: final / Resolution: 1.2→32.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 28 221 1296
Biso mean--7.97 19.01 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Rfactor Rfree error
1.2-1.23250.18441540.17372708100
1.2325-1.26870.1641460.160727061000
1.2687-1.30970.16981270.15742680980
1.3097-1.35650.16671360.151927291000
1.3565-1.41080.16941520.152827151000
1.4108-1.4750.16351390.14327381000
1.475-1.55280.1661510.14092708990
1.5528-1.65010.18211420.142727451000
1.6501-1.77740.17571500.149827541000
1.7774-1.95630.171400.153827591000
1.9563-2.23930.16591500.147827891000
2.2393-2.82110.15621460.163628121000
2.8211-32.8990.15561570.144629441000

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