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- PDB-8jah: Crystal structure of human CLEC12A C-type lectin domain -

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Basic information

Entry
Database: PDB / ID: 8jah
TitleCrystal structure of human CLEC12A C-type lectin domain
ComponentsC-type lectin domain family 12 member A
KeywordsSTRUCTURAL PROTEIN / Receptor
Function / homology
Function and homology information


signaling receptor regulator activity / tertiary granule membrane / specific granule membrane / transmembrane signaling receptor activity / carbohydrate binding / Neutrophil degranulation / signal transduction / plasma membrane
Similarity search - Function
C-type lectin domain family 12 member A/B / Natural killer cell receptor-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 12 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLei, Q. / Tang, H. / Dong, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171254 China
National Natural Science Foundation of China (NSFC)32201007 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Mechanistic insights into the C-type lectin receptor CLEC12A-mediated immune recognition of monosodium urate crystal.
Authors: Tang, H. / Xiao, Y. / Qian, L. / Wang, Z. / Lu, M. / Yao, N. / Zhou, T. / Tian, F. / Cao, L. / Zheng, P. / Dong, X.
History
DepositionMay 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type lectin domain family 12 member A
B: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2265
Polymers28,9952
Non-polymers2313
Water1,20767
1
A: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6333
Polymers14,4981
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5942
Polymers14,4981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.012, 50.012, 367.627
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein C-type lectin domain family 12 member A / C-type lectin-like molecule 1 / CLL-1 / Dendritic cell-associated lectin 2 / DCAL-2 / Myeloid ...C-type lectin-like molecule 1 / CLL-1 / Dendritic cell-associated lectin 2 / DCAL-2 / Myeloid inhibitory C-type lectin-like receptor / MICL


Mass: 14497.507 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC12A, CLL1, DCAL2, MICL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5QGZ9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M Potassium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationMonochromator: PILATUS XXX, S/N XX-XXX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.58→43.01 Å / Num. obs: 8840 / % possible obs: 92.38 % / Redundancy: 13.4 % / Biso Wilson estimate: 43.56 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 13.357
Reflection shellResolution: 2.58→2.67 Å / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.462 / Num. unique obs: 751

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→43.01 Å / SU ML: 0.2701 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 24.5232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 419 4.74 %
Rwork0.2049 8421 -
obs0.2076 8840 92.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.82 Å2
Refinement stepCycle: LAST / Resolution: 2.58→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 11 67 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282086
X-RAY DIFFRACTIONf_angle_d0.58682820
X-RAY DIFFRACTIONf_chiral_restr0.0411284
X-RAY DIFFRACTIONf_plane_restr0.0041356
X-RAY DIFFRACTIONf_dihedral_angle_d5.0546276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.950.33061160.25142543X-RAY DIFFRACTION86.61
2.95-3.720.2821430.21732744X-RAY DIFFRACTION92.8
3.72-43.010.23461600.18653134X-RAY DIFFRACTION96.88

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