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- PDB-8h4v: Mincle CRD complex with PGL trisaccharide -

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Basic information

Entry
Database: PDB / ID: 8h4v
TitleMincle CRD complex with PGL trisaccharide
ComponentsC-type lectin domain family 4 member E
KeywordsSUGAR BINDING PROTEIN / Immune receptor / Innate immunity / C-type lectin receptor / Mycobacterium leprae
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 / 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
C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

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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
B: C-type lectin domain family 4 member E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,18510
Polymers34,8872
Non-polymers1,2988
Water0
1
A: C-type lectin domain family 4 member E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0925
Polymers17,4441
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area7930 Å2
MethodPISA
2
B: C-type lectin domain family 4 member E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0925
Polymers17,4441
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.298, 75.298, 111.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z

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Components

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


Mass: 17443.527 Da / Num. of mol.: 2
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 (2~{R},3~{R},4~{S},5~{S},6~{R})-6-(methoxymethyl)oxane-2,3,4,5-tetrol-(1-4)-6-deoxy-2,3-di-O-methyl- ...(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(methoxymethyl)oxane-2,3,4,5-tetrol-(1-4)-6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose-(1-2)-3-O-methyl-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 528.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][a-L-Rhap3Me]{[(2+1)][a-L-Rhap2Me3Me]{[(4+1)][b-D-Glcp6Me]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M imidazole (pH 7.5), 0.2M sodium acetate trihydrate, 10%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→42.36 Å / Num. obs: 14310 / % possible obs: 100 % / Redundancy: 40.2 % / Biso Wilson estimate: 76.34 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.021 / Net I/σ(I): 18
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 42.6 % / Rmerge(I) obs: 4.059 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 14310 / CC1/2: 0.601 / Rpim(I) all: 0.627 / % possible all: 100

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Processing

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

4zrw


Resolution: 2.4→42.35 Å / SU ML: 0.4518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2886 710 4.96 %
Rwork0.2563 13600 -
obs0.2578 14310 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 78 0 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052518
X-RAY DIFFRACTIONf_angle_d0.78623423
X-RAY DIFFRACTIONf_chiral_restr0.0478367
X-RAY DIFFRACTIONf_plane_restr0.0066429
X-RAY DIFFRACTIONf_dihedral_angle_d6.5924308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.46711310.39832717X-RAY DIFFRACTION99.96
2.59-2.850.42141360.35412691X-RAY DIFFRACTION100
2.85-3.260.33971390.32312714X-RAY DIFFRACTION99.69
3.26-4.10.30561340.27262691X-RAY DIFFRACTION98.26
4.1-42.350.25411700.21622787X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 24.8191781502 Å / Origin y: 5.54886933536 Å / Origin z: -17.9022935827 Å
111213212223313233
T0.432666225409 Å20.222064710961 Å2-0.0382470049943 Å2-0.82064775734 Å2-0.00854089113879 Å2--0.620770553949 Å2
L1.50036682895 °2-0.39926385748 °20.760714558254 °2-0.247139080983 °20.52338862864 °2--3.53023605438 °2
S0.158150545385 Å °0.703953907916 Å °0.369913392514 Å °-0.0733138759923 Å °-0.0521233598952 Å °-0.426639977524 Å °-0.113014071913 Å °0.350928943541 Å °-0.0833470199238 Å °
Refinement TLS groupSelection details: all

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