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- PDB-3wh3: human Mincle, ligand free form -

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Basic information

Entry
Database: PDB / ID: 3wh3
Titlehuman Mincle, ligand free form
ComponentsC-type lectin domain family 4 member E
KeywordsIMMUNE SYSTEM / c-type lectin / carbohydrate recognition / glycolipid binding / Plasmamembrane
Function / homology
Function and homology information


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 / phagocytic cup / Dectin-2 family / cell projection / positive regulation of cytokine production ...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 / phagocytic cup / Dectin-2 family / cell projection / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding / defense response to bacterium / external side of plasma membrane / innate immune response / calcium ion binding / membrane / plasma membrane
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
C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsFurukawa, A. / Kamishikiryo, J. / Mori, D. / Toyonaga, K. / Okabe, Y. / Toji, A. / Kanda, R. / Miyake, Y. / Ose, T. / Yamasaki, S. / Maenaka, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL
Authors: Furukawa, A. / Kamishikiryo, J. / Mori, D. / Toyonaga, K. / Okabe, Y. / Toji, A. / Kanda, R. / Miyake, Y. / Ose, T. / Yamasaki, S. / Maenaka, K.
History
DepositionAug 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-type lectin domain family 4 member E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9583
Polymers16,8781
Non-polymers802
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.074, 49.074, 43.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein C-type lectin domain family 4 member E / C-type lectin superfamily member 9 / Macrophage-inducible C-type lectin


Mass: 16878.072 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 74-219 / Mutation: I99K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4E / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9ULY5
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 1.77 Å3/Da / Density % sol: 30.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris propane, 0.2M potassium thiocyanate, 20%(w/v) PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2012 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→24.54 Å / Num. obs: 27209 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 5.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.7
Reflection shellResolution: 1.32→1.367 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2690 / % possible all: 98.53

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FM5

1fm5


Resolution: 1.32→24.537 Å / SU ML: 0.15 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 1381 5.08 %random
Rwork0.1373 ---
obs0.1391 27209 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.615 Å2
Refinement stepCycle: LAST / Resolution: 1.32→24.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 2 165 1227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061093
X-RAY DIFFRACTIONf_angle_d1.1331480
X-RAY DIFFRACTIONf_chiral_restr0.077154
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d10.538387
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 (%)
1.32-1.36720.31781430.2982547269099
1.3672-1.42190.2191270.166625952722100
1.4219-1.48660.1781360.115826232759100
1.4866-1.5650.16131290.118725472676100
1.565-1.6630.17611310.12225732704100
1.663-1.79140.15711440.111126172761100
1.7914-1.97160.14141430.11325932736100
1.9716-2.25670.13831390.122325812720100
2.2567-2.84250.16581370.146725842721100
2.8425-24.54120.18391520.146925682720100

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