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- PDB-5vyb: Structure of the carbohydrate recognition domain of Dectin-2 comp... -

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Basic information

Entry
Database: PDB / ID: 5vyb
TitleStructure of the carbohydrate recognition domain of Dectin-2 complexed with a mammalian-type high mannose Man9GlcNAc2 oligosaccharide
ComponentsC-type lectin domain family 6 member A
KeywordsSUGAR BINDING PROTEIN / carbohydrate-binding protein / lectin / glycoprotein
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 / : / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 ...CD209-like, C-type lectin-like domain / : / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / C-type lectin domain family 6 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFeinberg, H. / Jegouzo, S.A.F. / Rex, M.J. / Drickamer, K. / Taylor, M.E. / Weis, W.I.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/K007718/1 United Kingdom
Wellcome Trust United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM62116 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Mechanism of pathogen recognition by human dectin-2.
Authors: Feinberg, H. / Jegouzo, S.A.F. / Rex, M.J. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Data collection / Database references
Category: citation / diffrn_detector / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_detector.detector / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Mar 21, 2018Group: Derived calculations / Category: struct_conn
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 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
A: C-type lectin domain family 6 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3136
Polymers16,9511
Non-polymers1,3625
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.055, 78.834, 76.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 16950.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the N-terminal ALA is a result of cloning / Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC6A, CLECSF10, DECTIN2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6EIG7
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2-2-2/a3-b1_a6-e1_b2-c1_c2-d1_e3-f1_f2-g1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drop size: 0.9:0.9 micro-liter of protein:reservoir protein solution: 2 mg/ml CRD, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, and 2 mM Man9GlcNAc2. The reservoir solution: 1.0 M NaCl, 6% ...Details: Drop size: 0.9:0.9 micro-liter of protein:reservoir protein solution: 2 mg/ml CRD, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, and 2 mM Man9GlcNAc2. The reservoir solution: 1.0 M NaCl, 6% polyethylene glycol 400 and 0.1 M Tris-Cl, pH 8.0. freezing solution: 30% polyethylene glycol 400, 1.0 M NaCl, 0.1 M Tris-Cl, pH 8.0, and 2 mM Man9GlcNAc2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2017
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.39→38.23 Å / Num. obs: 7880 / % possible obs: 99.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 37.47 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.038 / Rrim(I) all: 0.088 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1 / % possible all: 97.3

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
2.39-2.485.10.4320.9310.2070.482
8.95-38.234.30.0490.9080.0290.057

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZRV

4zrv


Resolution: 2.4→38.229 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / Phase error: 32.13
Details: custom non-bonded symmetry exclusions added for the mannose residues
RfactorNum. reflection% reflection
Rfree0.2404 390 5 %
Rwork0.2052 --
obs0.2069 7793 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.27 Å2 / Biso mean: 45.7093 Å2 / Biso min: 25.06 Å2
Refinement stepCycle: final / Resolution: 2.4→38.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 88 19 1269
Biso mean--48.29 40.34 -
Num. residues----143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071312
X-RAY DIFFRACTIONf_angle_d0.5281766
X-RAY DIFFRACTIONf_chiral_restr0.039196
X-RAY DIFFRACTIONf_plane_restr0.002209
X-RAY DIFFRACTIONf_dihedral_angle_d12.535768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4002-2.74750.32711260.25022404253099
2.7475-3.46120.23071300.224624552585100
3.4612-38.23430.2211340.18532544267899

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