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- PDB-4zrv: Structure of cow mincle CRD complexed with trehalose mono butyrate -

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Basic information

Entry
Database: PDB / ID: 4zrv
TitleStructure of cow mincle CRD complexed with trehalose mono butyrate
ComponentsMincle CRD
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 / glycolipid binding / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding ...Dectin-2 family / T cell differentiation involved in immune response / glycolipid binding / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor signaling pathway / pattern recognition receptor activity / 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 ...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
6-butanoyl-trehalose / ACETATE ION / C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.095 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: Advisory / Atomic model ...Advisory / 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_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / 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_alt_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.pdbx_formal_charge / _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_assembly_gen.asym_id_list / _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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_entity_branch_link
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_branch_link.leaving_atom_id_2
Revision 2.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mincle CRD
B: Mincle CRD
C: Mincle CRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,99718
Polymers47,2223
Non-polymers1,77515
Water6,702372
1
A: Mincle CRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3326
Polymers15,7411
Non-polymers5925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mincle CRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2735
Polymers15,7411
Non-polymers5334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mincle CRD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3917
Polymers15,7411
Non-polymers6516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-82 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.464, 46.676, 77.920
Angle α, β, γ (deg.)90.000, 101.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mincle CRD


Mass: 15740.721 Da / Num. of mol.: 3 / Fragment: unp residues 79-208
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 6-O-butanoyl-alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / 6-butanoyl-trehalose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 412.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 6-butanoyl-trehalose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1a_1-5_6*OCCCC/3=O]/1-2/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.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: protein solution: 2.1 mg/mL mincle, 2.5 mM CaCl2 and 33 mM tmb. Reservoir solution: 20% Peg 4K, 20% 2-Propanol and 0.1 M Sodium Acetate pH=5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.095→38.223 Å / Num. all: 27266 / Num. obs: 27266 / % possible obs: 98 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.2 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.096 / Rsym value: 0.085 / Net I/av σ(I): 8.812 / Net I/σ(I): 13.7 / Num. measured all: 122769
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.214.30.4671.71646538320.2490.4673.595.1
2.21-2.344.70.3692.11757337690.1890.3694.598.5
2.34-2.54.50.26331606935370.1370.2635.999.1
2.5-2.714.40.19441435032540.1030.1947.697.3
2.71-2.964.70.1361418130460.0670.131199
2.96-3.314.50.0799.71261927840.0410.07916.599.3
3.31-3.834.50.04715.31102124290.0250.04725.797.8
3.83-4.694.50.03619.3946221000.0190.03633.199.2
4.69-6.634.40.03619.5712116050.0190.03631.997.9
6.63-38.2234.30.02423.539089100.0130.02439.997

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementResolution: 2.095→38.223 Å / FOM work R set: 0.826 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1367 5.02 %
Rwork0.1632 25877 -
obs0.1655 27244 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.22 Å2 / Biso mean: 16.94 Å2 / Biso min: 3.57 Å2
Refinement stepCycle: final / Resolution: 2.095→38.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 97 372 3711
Biso mean--18.5 23.68 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143539
X-RAY DIFFRACTIONf_angle_d1.1064722
X-RAY DIFFRACTIONf_chiral_restr0.077499
X-RAY DIFFRACTIONf_plane_restr0.004619
X-RAY DIFFRACTIONf_dihedral_angle_d13.0211269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0954-2.17030.28811260.23972446257293
2.1703-2.25720.30341350.20962575271098
2.2572-2.35990.27211350.20042578271398
2.3599-2.48430.26171370.18542598273599
2.4843-2.63990.27671360.18282537267396
2.6399-2.84370.21771390.17032602274199
2.8437-3.12970.17711370.16122637277499
3.1297-3.58230.20711400.15592584272498
3.5823-4.51220.16141380.1282642278099
4.5122-38.22920.16131440.14812678282297

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