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- PDB-8rov: Human dectin-2 with dimerization domain -

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Basic information

Entry
Database: PDB / ID: 8rov
TitleHuman dectin-2 with dimerization domain
ComponentsC-type lectin domain family 6 member A
KeywordsSUGAR BINDING PROTEIN / Lectin / glycan-binding protein / cell signalling / innate immunity
Function / homology
Function and homology information


detection of yeast / antifungal innate immune response / response to yeast / positive regulation of T-helper 17 type immune response / pattern recognition receptor activity / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / D-mannose binding / phospholipase binding / positive regulation of intracellular signal transduction ...detection of yeast / antifungal innate immune response / response to yeast / positive regulation of T-helper 17 type immune response / pattern recognition receptor activity / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / D-mannose binding / phospholipase binding / positive regulation of intracellular signal transduction / defense response to fungus / positive regulation of cytokine production / carbohydrate binding / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / external side of plasma membrane / innate immune response / calcium ion binding / plasma membrane
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
methyl alpha-D-mannopyranoside / C-type lectin domain family 6 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLiu, Y. / Kim, J.W. / Feinberg, H. / Cull, N. / Weis, W.I. / Taylor, M.E. / Drickamer, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/V014137/1 United Kingdom
CitationJournal: Glycobiology / Year: 2024
Title: Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers.
Authors: Liu, Y. / Kim, J.W. / Feinberg, H. / Cull, N. / Weis, W.I. / Taylor, M.E. / Drickamer, K.
History
DepositionJan 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-type lectin domain family 6 member A
B: C-type lectin domain family 6 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,76610
Polymers44,1722
Non-polymers5958
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-75 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.211, 65.030, 81.582
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein C-type lectin domain family 6 member A / C-type lectin superfamily member 10 / Dendritic cell-associated C-type lectin 2 / DC-associated C- ...C-type lectin superfamily member 10 / Dendritic cell-associated C-type lectin 2 / DC-associated C-type lectin 2 / Dectin-2


Mass: 22085.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal alpha helical dimerization domain (residues 1 to 27 in chains A/B) added to extracellular domain (residues 28 to 194 in chains A/B)
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC6A, CLECSF10, DECTIN2 / Plasmid: pT5T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6EIG7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3.35K, 90 mM MES, pH 6.0, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.36→59.71 Å / Num. obs: 15183 / % possible obs: 96 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.57 Å2 / Rsym value: 0.114 / Net I/σ(I): 6.9
Reflection shellResolution: 2.36→2.45 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1527 / Rsym value: 0.576 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→40.09 Å / SU ML: 0.2936 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.4078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 754 5 %
Rwork0.2222 14328 -
obs0.2254 15082 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.69 Å2
Refinement stepCycle: LAST / Resolution: 2.36→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 32 21 2407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712456
X-RAY DIFFRACTIONf_angle_d0.88723336
X-RAY DIFFRACTIONf_chiral_restr0.0551336
X-RAY DIFFRACTIONf_plane_restr0.0076424
X-RAY DIFFRACTIONf_dihedral_angle_d15.9503842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.540.35431520.29142872X-RAY DIFFRACTION95.64
2.54-2.80.39841420.28042821X-RAY DIFFRACTION95.33
2.8-3.20.32261580.25512833X-RAY DIFFRACTION94.32
3.2-4.030.30061530.20812915X-RAY DIFFRACTION96.78
4.03-40.090.2141490.1882887X-RAY DIFFRACTION93.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5668828938280.5674343758660.1106731359716.094299769762.457990185783.9028256140.137884443841-0.02212249378110.04424931590170.0295451143193-0.1493734324960.0439137429580.0144180081307-0.16678506399-0.003341952700070.226427407320.0108330754434-0.0238727770.3430505770540.008363580427070.314140065179-17.835667229311.6216732903-12.9220066041
21.90406644379-2.3859113376-1.19867604357.009475313972.217617408512.674459478410.1318543040580.0616373101584-0.0400540330324-0.0794814261125-0.144940594630.22295058791-0.209218309613-0.109214683680.01495710129480.297423826409-0.0251835511291-0.01813495562390.3490535088450.02178987293030.339434354603-22.389273961652.573884003912.3049102146
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 62 - 403 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 62 through 403)AA - E
22(chain 'B' and resid 62 through 403)BF - J

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