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- PDB-8w8t: Crystal structure of human CLEC12A CRD -

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Basic information

Entry
Database: PDB / ID: 8w8t
TitleCrystal structure of human CLEC12A CRD
ComponentsC-type lectin domain family 12 member A
KeywordsIMMUNE SYSTEM / Pattern Recognition Receptor / Innate immunitiy / C-type lectin receptor / DAMPs
Function / homology
Function and homology information


negative regulation of dendritic cell differentiation / negative regulation of natural killer cell activation / negative regulation of immune response / signaling receptor regulator activity / negative regulation of neutrophil activation / pattern recognition receptor activity / tertiary granule membrane / specific granule membrane / positive regulation of type I interferon production / negative regulation of inflammatory response ...negative regulation of dendritic cell differentiation / negative regulation of natural killer cell activation / negative regulation of immune response / signaling receptor regulator activity / negative regulation of neutrophil activation / pattern recognition receptor activity / tertiary granule membrane / specific granule membrane / positive regulation of type I interferon production / negative regulation of inflammatory response / 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: 2.3 Å
AuthorsMori, S. / Nagae, M. / Yamasaki, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00505 Japan
CitationJournal: Int.Immunol. / Year: 2024
Title: Crystal structure of the complex of CLEC12A and an antibody that interferes with binding of diverse ligands.
Authors: Mori, S. / Nagae, M. / Yamasaki, S.
History
DepositionSep 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Structure summary / Category: 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 12 member A
B: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8626
Polymers29,4782
Non-polymers3844
Water1,62190
1
A: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9313
Polymers14,7391
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area7250 Å2
MethodPISA
2
B: C-type lectin domain family 12 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9313
Polymers14,7391
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.037, 50.037, 364.240
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
Components on special symmetry positions
IDModelComponents
11B-436-

HOH

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Components

#1: Protein C-type lectin domain family 12 member A


Mass: 14738.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC12A / Production host: Homo sapiens (human) / References: UniProt: Q5QGZ9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium cacodylate (pH 6.5), 0.2M Ammonium sulfate, 30% polyethylene glycol 8,000

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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: May 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→45.53 Å / Num. obs: 13302 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 30.59 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.062 / Rrim(I) all: 0.266 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1252 / CC1/2: 0.74 / Rpim(I) all: 0.343 / Rrim(I) all: 1.545 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.16 Å / SU ML: 0.3346 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2854 627 4.76 %
Rwork0.2346 12539 -
obs0.2371 13166 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 20 90 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00162110
X-RAY DIFFRACTIONf_angle_d0.42032856
X-RAY DIFFRACTIONf_chiral_restr0.0364286
X-RAY DIFFRACTIONf_plane_restr0.0038360
X-RAY DIFFRACTIONf_dihedral_angle_d4.2412278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.39671290.28563031X-RAY DIFFRACTION99.97
2.53-2.90.30471530.26433045X-RAY DIFFRACTION99.97
2.9-3.650.29521570.23213105X-RAY DIFFRACTION99.97
3.65-42.160.25021880.21153358X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -8.73189719608 Å / Origin y: 0.789731117558 Å / Origin z: -15.5052739975 Å
111213212223313233
T0.215115401793 Å2-0.0402285828589 Å20.00891785232 Å2-0.185600222629 Å2-0.0122547759245 Å2--0.169827856385 Å2
L2.27915682036 °2-0.36033857186 °2-0.0366180637186 °2-0.0568078463943 °2-0.00692366961886 °2--0.0342010352569 °2
S0.0210281231734 Å °-0.00572133365937 Å °0.0825758539308 Å °0.043381054327 Å °-0.0390677040957 Å °0.0181605057268 Å °-0.0133830712757 Å °0.000674494727695 Å °0.0356376695681 Å °
Refinement TLS groupSelection details: all

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