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- PDB-8a59: C-type lectin-like domain (CTLD) and Sushi-like domain of human CD93 -

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Basic information

Entry
Database: PDB / ID: 8a59
TitleC-type lectin-like domain (CTLD) and Sushi-like domain of human CD93
ComponentsComplement component C1q receptor
KeywordsCELL ADHESION / C-type lectin-like domain / CTLD / Sushi-like domain / dimerization / angiogenesis / CD93
Function / homology
Function and homology information


complement component C1q complex binding / macrophage activation / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / phagocytosis / secretory granule membrane / cell-cell adhesion / signaling receptor activity / carbohydrate binding ...complement component C1q complex binding / macrophage activation / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / phagocytosis / secretory granule membrane / cell-cell adhesion / signaling receptor activity / carbohydrate binding / membrane => GO:0016020 / calcium ion binding / Neutrophil degranulation / cell surface / plasma membrane
Similarity search - Function
Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF 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 / EGF-type aspartate/asparagine hydroxylation site ...Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF 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 / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Complement component C1q receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTassone, G. / Barbera, S. / Raucci, L. / Orlandini, M. / Pozzi, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Dimerization of the C-type lectin-like receptor CD93 promotes its binding to Multimerin-2 in endothelial cells.
Authors: Barbera, S. / Raucci, L. / Tassone, G. / Tinti, L. / Prischi, F. / Santucci, A. / Mongiat, M. / Tosi, G.M. / Galvagni, F. / Dimberg, A. / Pozzi, C. / Orlandini, M.
History
DepositionJun 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement component C1q receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,44210
Polymers25,6011
Non-polymers8419
Water1,44180
1
A: Complement component C1q receptor
hetero molecules

A: Complement component C1q receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88320
Polymers51,2022
Non-polymers1,68218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area5510 Å2
ΔGint-111 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.712, 112.504, 73.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-309-

SO4

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Components

#1: Protein Complement component C1q receptor / C1q/MBL/SPA receptor / C1qR / C1qR(p) / C1qRp / CDw93 / Complement component 1 q subcomponent ...C1q/MBL/SPA receptor / C1qR / C1qR(p) / C1qRp / CDw93 / Complement component 1 q subcomponent receptor 1 / Matrix-remodeling-associated protein 4


Mass: 25600.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD93, C1QR1, MXRA4 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NPY3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Ammonium sulfate, 1 M Lithium sulfate and 0.1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 9, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→73.26 Å / Num. obs: 20515 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.022 / Rrim(I) all: 0.076 / Net I/σ(I): 12.3
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.226 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2956 / CC1/2: 0.83 / Rpim(I) all: 0.356 / Rrim(I) all: 1.278 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q9NPY3-F1

Resolution: 1.92→55.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.295 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 1056 5.2 %RANDOM
Rwork0.2088 ---
obs0.212 19418 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.01 Å2 / Biso mean: 57.272 Å2 / Biso min: 33.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.2699 Å
Refinement stepCycle: final / Resolution: 1.92→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 51 80 1761
Biso mean--76.48 62.18 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121725
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.632336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8145220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55622.65664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44915252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.308156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021257
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 82 -
Rwork0.301 1392 -
all-1474 -
obs--99.39 %

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