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- PDB-4kzv: Structure of the carbohydrate-recognition domain of the C-type le... -

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Basic information

Entry
Database: PDB / ID: 4kzv
TitleStructure of the carbohydrate-recognition domain of the C-type lectin mincle bound to trehalose
ComponentsC-type lectin mincle
KeywordsCARBOHYDRATE-BINDING PROTEIN / C-type lectin / carbohydrate-recognition domain
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
trehalose / C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFeinberg, H. / Jegouzo, S.A.F. / Rowntree, T.J.W. / Guan, Y. / Brash, M.A. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Mechanism for Recognition of an Unusual Mycobacterial Glycolipid by the Macrophage Receptor Mincle.
Authors: Feinberg, H. / Jegouzo, S.A. / Rowntree, T.J. / Guan, Y. / Brash, M.A. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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 / _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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: C-type lectin mincle
B: C-type lectin mincle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0078
Polymers31,4812
Non-polymers5266
Water4,918273
1
A: C-type lectin mincle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1865
Polymers15,7411
Non-polymers4454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-type lectin mincle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8213
Polymers15,7411
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.48, 73.48, 99.34
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-507-

HOH

21B-520-

HOH

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Components

#1: Protein C-type lectin mincle


Mass: 15740.721 Da / Num. of mol.: 2
Fragment: carbohydrate recognition domain (UNP residues 79-208)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLEC4E / Plasmid: pT5T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE SEQUENCE MATCHES NCBI SEQUENCE XM_592701.4, AND THE CONFLICT AT RESIDUE 174 ...AUTHORS STATE THAT THE SEQUENCE MATCHES NCBI SEQUENCE XM_592701.4, AND THE CONFLICT AT RESIDUE 174 IS A KNOWN POLYMORPHISM.

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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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein: 2.5 mg/ml mincle, 2.5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, 50 mM Trehalose. Reservoir: 25% polyethylene glycol 4,000, 17.5% 2-propanol and 0.1 M sodium citrate, pH 5.0, ...Details: Protein: 2.5 mg/ml mincle, 2.5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, 50 mM Trehalose. Reservoir: 25% polyethylene glycol 4,000, 17.5% 2-propanol and 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→36.74 Å / Num. obs: 54041 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 9.6 % / Rsym value: 0.034 / Net I/σ(I): 29.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.489.70.3422.37480076980.34299
1.48-1.579.60.2223.57088273610.222100
1.57-1.679.70.145.66775669600.14100
1.67-1.819.80.0928.46348664560.092100
1.81-1.989.50.05812.65712460010.058100
1.98-2.219.90.04316.25373354460.043100
2.21-2.569.30.03618.74489448120.03699.9
2.56-3.139.60.0321.93954741190.03100
3.13-4.438.90.02426.32907932690.02499.9
4.43-36.7398.60.02127.71644419190.02199.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
Blu-IceIcedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→36.74 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8713 / SU ML: 0.14 / σ(F): 0 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 2694 4.99 %
Rwork0.17 --
obs-53969 99.8 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.78 Å2 / Biso mean: 29.2 Å2 / Biso min: 9.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 28 273 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012267
X-RAY DIFFRACTIONf_angle_d0.9813044
X-RAY DIFFRACTIONf_chiral_restr0.067313
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d11.089815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42630.24521320.18682581271397
1.4263-1.45380.25451410.184126722813100
1.4538-1.48340.23691400.187826512791100
1.4834-1.51570.24841390.187126422781100
1.5157-1.5510.23471410.181726872828100
1.551-1.58980.22621400.179326552795100
1.5898-1.63270.23561410.173726712812100
1.6327-1.68080.22511400.168526672807100
1.6808-1.7350.21011420.166326822824100
1.735-1.7970.22521410.176126872828100
1.797-1.8690.23161410.172526822823100
1.869-1.9540.20251410.170826842825100
1.954-2.05710.2411420.164827052847100
2.0571-2.18590.2041430.169526952838100
2.1859-2.35470.20421420.166427152857100
2.3547-2.59160.21251430.177327152858100
2.5916-2.96640.22781440.183327522896100
2.9664-3.73680.21161480.166127962944100
3.7368-36.75190.16091530.158929363089100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0847-0.00850.03670.001-0.00320.01540.0757-0.0005-0.0313-0.02560.01650.03130.00360.00190.02510.62070.16120.11130.17210.13920.3453-0.0202-10.428115.6237
20.0297-0.0197-0.01850.01920.02370.01640.10260.0803-0.0046-0.2969-0.1245-0.0120.39420.0495-0.06640.50840.05680.16850.0960.12150.2573-5.4884-4.390313.6706
30.00050.0058-0.00410.0870.01560.0847-0.0923-0.0027-0.0485-0.0391-0.04530.04660.16460.0023-0.14730.2334-0.0260.04710.17540.05420.2325-10.9845-0.51724.2765
40.0268-0.0262-0.01990.03530.03220.03360.0077-0.0274-0.0253-0.0493-0.0757-0.0720.01930.0562-0.0050.25010.02750.14220.13710.12130.1676-4.21144.719415.2856
50.0419-0.05270.04680.0716-0.0490.0568-0.0040.03740.0331-0.0141-0.0498-0.04170.02260.0472-0.04850.7050.16250.14570.07990.17470.026-4.60981.99833.3662
60.0148-0.0219-0.00640.0540.02320.0033-0.00030.01150.0174-0.0673-0.00670.04130.082-0.032-0.00710.3301-0.1416-0.07080.0717-0.03380.1187-14.9561-3.40639.1458
70.0051-0.0194-0.00840.06930.02080.0072-0.0416-0.04970.08010.0135-0.00250.0711-0.0696-0.0704-0.01880.2540.1789-0.02130.30260.0280.2934-16.561914.915517.5143
80.0409-0.0255-0.00830.02250.00120.0022-0.0373-0.00350.0135-0.0884-0.07320.0615-0.04840.0515-0.06880.19950.01470.01310.16180.04930.158-6.743113.904213.9589
90.004-0.0017-0.00360.0048-0.0005-0.00170.0554-0.0310.0027-0.13950.13230.14250.0605-0.1503-0.00010.32090.0081-0.07560.25590.06850.2814-18.395610.42686.8005
100.01520.0011-0.00290.0009-0.01080.0580.0312-0.0622-0.0061-0.1823-0.01960.0410.0428-0.0510.00140.5626-0.2472-0.24840.1606-0.12080.1534-14.13164.12043.2632
110.0081-0.0112-0.02090.00820.02550.0621-0.0578-0.04150.115-0.0828-0.00130.2546-0.0085-0.27440.00290.3098-0.1243-0.09320.31070.05870.3262-19.44321.77514.6903
120.10890.02290.03760.02750.02540.05830.0019-0.0199-0.0229-0.0272-0.0206-0.08060.08290.07880.06180.36470.06390.2441-0.0490.28280.14350.317-2.143418.0057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN B AND (RESID 78:83 )B0
2X-RAY DIFFRACTION2CHAIN B AND (RESID 84:99 )B0
3X-RAY DIFFRACTION3CHAIN B AND (RESID 100:110 )B0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 111:119 )B0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 120:129 )B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 130:139 )B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 140:149 )B0
8X-RAY DIFFRACTION8CHAIN B AND (RESID 150:161 )B0
9X-RAY DIFFRACTION9CHAIN B AND (RESID 162:177 )B0
10X-RAY DIFFRACTION10CHAIN B AND (RESID 178:190 )B0
11X-RAY DIFFRACTION11CHAIN B AND (RESID 191:202 )B0
12X-RAY DIFFRACTION12CHAIN B AND (RESID 203:209 )B0

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