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- PDB-4zrw: Structure of cow mincle complexed with trehalose -

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Basic information

Entry
Database: PDB / ID: 4zrw
TitleStructure of cow mincle complexed with trehalose
Componentsmincle proteinMincle receptor
KeywordsSUGAR BINDING PROTEIN / glycobiology / carbohydrate-binding protein / C-type lectin / complex
Function / homology
Function and homology information


Dectin-2 family / T cell differentiation involved in immune response / antifungal innate immune response / glycolipid binding / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / pattern recognition receptor signaling pathway / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding ...Dectin-2 family / T cell differentiation involved in immune response / antifungal innate immune response / glycolipid binding / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / pattern recognition receptor signaling pathway / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding / defense response to bacterium / external side of plasma membrane / calcium ion binding
Similarity search - Function
CD209-like, C-type lectin-like domain / 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
trehalose / C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsFeinberg, H. / Rambaruth, N.D.S. / Taylor, M.E. / Drickamer, K. / Weis, W.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093599 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Binding Sites for Acylated Trehalose Analogs of Glycolipid Ligands on an Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle.
Authors: Feinberg, H. / Rambaruth, N.D. / Jegouzo, S.A. / Jacobsen, K.M. / Djurhuus, R. / Poulsen, T.B. / Weis, W.I. / Taylor, M.E. / Drickamer, K.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mincle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7625
Polymers17,2991
Non-polymers4634
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.800, 97.800, 45.200
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 mincle protein / Mincle receptor


Mass: 17299.396 Da / Num. of mol.: 1 / Fragment: unp residues 64-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLEC4E / Production host: Escherichia coli (E. coli) / References: UniProt: E1BHM0
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THE CORRECT SEQUENCE HAS BEEN DEPOSITED AT THE NCBI: SEQUENCE XM_592701.4

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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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: protein solution: 7.2 mg/mL mincle, 5 mM CaCl2, 10 mM Tris (pH 8.0), 25 mM NaCl and 30 mM trehalose. Reservoir solution: 2% Peg 3.35K, 0.2 MgCl2, 0.1 M Tris pH=8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→48.9 Å / Num. obs: 7737 / % possible obs: 98.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 40.87 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.054 / Net I/σ(I): 9.7 / Num. measured all: 33591 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.6-2.7240.4812.337159260.7590.27197.4
9.01-48.94.20.04920.18722080.9970.02698.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.1.26data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 2.6→42.349 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 358 4.63 %
Rwork0.1521 7373 -
obs0.1546 7731 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.61 Å2 / Biso mean: 43.1986 Å2 / Biso min: 25.15 Å2
Refinement stepCycle: final / Resolution: 2.6→42.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 26 56 1276
Biso mean--40.48 40.51 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151279
X-RAY DIFFRACTIONf_angle_d1.1581702
X-RAY DIFFRACTIONf_chiral_restr0.044180
X-RAY DIFFRACTIONf_plane_restr0.005216
X-RAY DIFFRACTIONf_dihedral_angle_d14.414459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6002-2.97630.29071170.21682409252698
2.9763-3.74950.2521200.16542434255498
3.7495-42.35420.15451210.12372530265199

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