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- PDB-8hb5: Crystal structure of Mincle in complex with HD-275 -

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Basic information

Entry
Database: PDB / ID: 8hb5
TitleCrystal structure of Mincle in complex with HD-275
ComponentsC-type lectin domain family 4 member E
KeywordsIMMUNE SYSTEM / Innate immunity / C-type lectin receptors / Mycobacterium leprae
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 / : / 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
Similarity search - Domain/homology
Chem-L6N / C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIshizuka, S. / Nagae, M. / Yamasaki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00505 Japan
Japan Society for the Promotion of Science (JSPS)20K06575 Japan
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: PGL-III, a Rare Intermediate of Mycobacterium leprae Phenolic Glycolipid Biosynthesis, Is a Potent Mincle Ligand.
Authors: Ishizuka, S. / van Dijk, J.H.M. / Kawakita, T. / Miyamoto, Y. / Maeda, Y. / Goto, M. / Le Calvez, G. / Groot, L.M. / Witte, M.D. / Minnaard, A.J. / van der Marel, G.A. / Ato, M. / Nagae, M. ...Authors: Ishizuka, S. / van Dijk, J.H.M. / Kawakita, T. / Miyamoto, Y. / Maeda, Y. / Goto, M. / Le Calvez, G. / Groot, L.M. / Witte, M.D. / Minnaard, A.J. / van der Marel, G.A. / Ato, M. / Nagae, M. / Codee, J.D.C. / Yamasaki, S.
History
DepositionOct 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

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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)17,7585
Polymers17,4441
Non-polymers3144
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.515, 97.515, 46.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein C-type lectin domain family 4 member E


Mass: 17443.527 Da / Num. of mol.: 1 / Mutation: I174T
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-L6N / (2~{R},3~{R},4~{S},5~{S},6~{R})-6-(methoxymethyl)oxane-2,3,4,5-tetrol


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M immidazole (pH 8.0), 0.2M sodium acetate trihydrate, 10% PEG8,000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1951N
2951N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-1A11.0344
SYNCHROTRONPhoton Factory BL-17A21
Detector
TypeIDDetectorDate
DECTRIS EIGER X 4M1PIXELJun 4, 2022
DECTRIS EIGER X 16M2PIXELJun 17, 2022
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(1 1 1)SINGLE WAVELENGTHMx-ray1
2Si (1 1 1)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03441
211
ReflectionResolution: 2.6→48.76 Å / Num. obs: 8053 / % possible obs: 100 % / Redundancy: 50.3 % / Biso Wilson estimate: 47.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.379 / Rpim(I) all: 0.054 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 50.5 % / Rmerge(I) obs: 3.705 / Num. unique obs: 8053 / CC1/2: 0.878 / Rpim(I) all: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZRW

4zrw


Resolution: 2.6→48.76 Å / SU ML: 0.3322 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.8575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3356 422 5.24 %
Rwork0.2956 7631 -
obs0.2977 8053 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 16 3 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241242
X-RAY DIFFRACTIONf_angle_d0.52741685
X-RAY DIFFRACTIONf_chiral_restr0.0374175
X-RAY DIFFRACTIONf_plane_restr0.0075216
X-RAY DIFFRACTIONf_dihedral_angle_d5.1774155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.35911240.3492508X-RAY DIFFRACTION99.77
2.98-3.750.32861500.29942521X-RAY DIFFRACTION100
3.75-48.760.33271480.28012602X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: 35.4932986743 Å / Origin y: -36.0251419166 Å / Origin z: 2.45773564601 Å
111213212223313233
T0.199623709961 Å2-0.0433676605767 Å20.0258991888874 Å2-0.326458290373 Å20.0292466545628 Å2--0.240580845433 Å2
L2.61170384142 °20.0435322214761 °20.156321219889 °2-3.35296573143 °2-0.0875690460847 °2--2.9881279136 °2
S-0.192726074349 Å °-0.17620172657 Å °-0.0766288999637 Å °0.144518071227 Å °0.213462549414 Å °0.16734857929 Å °0.215874180203 Å °-0.469060010666 Å °-0.0237268847356 Å °
Refinement TLS groupSelection details: all

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