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- PDB-8w9j: Crystal structure of human CLEC12A ectodomain complexed with 50C1 Fab -

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Basic information

Entry
Database: PDB / ID: 8w9j
TitleCrystal structure of human CLEC12A ectodomain complexed with 50C1 Fab
Components
  • Anti-human CLEC12A antibody 50C1 heavy chain
  • Anti-human CLEC12A antibody 50C1 light chain
  • C-type lectin domain family 12 member A
KeywordsIMMUNE SYSTEM / C-type lectin receptor / inhibitory antibody / CLEC12A
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 / positive regulation of type I interferon production / specific granule membrane / 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 / positive regulation of type I interferon production / specific granule membrane / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 5, 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Anti-human CLEC12A antibody 50C1 light chain
H: Anti-human CLEC12A antibody 50C1 heavy chain
A: Anti-human CLEC12A antibody 50C1 light chain
B: Anti-human CLEC12A antibody 50C1 heavy chain
C: C-type lectin domain family 12 member A
D: C-type lectin domain family 12 member A


Theoretical massNumber of molelcules
Total (without water)143,0046
Polymers143,0046
Non-polymers00
Water00
1
L: Anti-human CLEC12A antibody 50C1 light chain
H: Anti-human CLEC12A antibody 50C1 heavy chain
C: C-type lectin domain family 12 member A


Theoretical massNumber of molelcules
Total (without water)71,5023
Polymers71,5023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Anti-human CLEC12A antibody 50C1 light chain
B: Anti-human CLEC12A antibody 50C1 heavy chain
D: C-type lectin domain family 12 member A


Theoretical massNumber of molelcules
Total (without water)71,5023
Polymers71,5023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.356, 45.142, 202.749
Angle α, β, γ (deg.)90.000, 93.130, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Anti-human CLEC12A antibody 50C1 light chain


Mass: 23694.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Anti-human CLEC12A antibody 50C1 heavy chain


Mass: 23900.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein C-type lectin domain family 12 member A


Mass: 23906.494 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
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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES-Na (pH 7.5), 0.2 M sodium chloride, 12% (w/v) PEG8000

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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: 3.5→43.54 Å / Num. obs: 19367 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 68.99 Å2 / CC1/2: 0.981 / Rpim(I) all: 0.115 / Net I/σ(I): 4.8
Reflection shellResolution: 3.5→3.83 Å / Num. unique obs: 4549 / CC1/2: 0.773 / Rpim(I) all: 0.328

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→42.13 Å / SU ML: 0.4813 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.7936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2913 976 5.04 %
Rwork0.2538 18373 -
obs0.2557 19349 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.7 Å2
Refinement stepCycle: LAST / Resolution: 3.5→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9192 0 0 0 9192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229416
X-RAY DIFFRACTIONf_angle_d0.549712786
X-RAY DIFFRACTIONf_chiral_restr0.04091392
X-RAY DIFFRACTIONf_plane_restr0.00521636
X-RAY DIFFRACTIONf_dihedral_angle_d4.97031274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.680.3131520.3252564X-RAY DIFFRACTION98.62
3.68-3.920.35381260.31082555X-RAY DIFFRACTION98.39
3.92-4.220.33241350.27422608X-RAY DIFFRACTION99.67
4.22-4.640.29511390.2462621X-RAY DIFFRACTION99.82
4.64-5.310.28451390.23462638X-RAY DIFFRACTION99.68
5.31-6.690.27851270.24742671X-RAY DIFFRACTION99.5
6.69-42.130.24241580.20752716X-RAY DIFFRACTION98.36
Refinement TLS params.Method: refined / Origin x: 81.1730927584 Å / Origin y: -49.247454794 Å / Origin z: -69.2631292859 Å
111213212223313233
T0.497598822556 Å2-0.0157171626302 Å2-0.0549688511684 Å2-0.383470712307 Å20.00116835439417 Å2--0.479522896937 Å2
L0.418144125634 °2-0.153583900679 °2-0.579762760328 °2-0.0587119740319 °20.266808800623 °2--0.820674586949 °2
S0.0115296757147 Å °-0.0138238098347 Å °-0.0101873793065 Å °-0.0884475816457 Å °-0.0503749669358 Å °0.0382458484612 Å °-0.0171977322317 Å °0.000873734744426 Å °0.0742936461328 Å °
Refinement TLS groupSelection details: all

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