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- PDB-2bpd: STRUCTURE OF MURINE DECTIN-1 -

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Basic information

Entry
Database: PDB / ID: 2bpd
TitleSTRUCTURE OF MURINE DECTIN-1
ComponentsDECTIN-1
KeywordsRECEPTOR / DECTIN-1 / BETA-GLUCAN / FUNGAL RECOGNITION / C-TYPE LECTIN-LIKE DOMAIN / CTLD / CARBOHYDRATE
Function / homology
Function and homology information


(1->3)-beta-D-glucan immune receptor activity / detection of molecule of fungal origin / detection of yeast / (1->3)-beta-D-glucan binding / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production / cell surface pattern recognition receptor signaling pathway / opsonin binding / antifungal innate immune response ...(1->3)-beta-D-glucan immune receptor activity / detection of molecule of fungal origin / detection of yeast / (1->3)-beta-D-glucan binding / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production / cell surface pattern recognition receptor signaling pathway / opsonin binding / antifungal innate immune response / positive regulation of interleukin-23 production / positive regulation of cytokine production involved in immune response / CLEC7A (Dectin-1) signaling / response to yeast / leukocyte activation involved in immune response / positive regulation of stress-activated MAPK cascade / cell activation / phagocytosis, recognition / cellular response to molecule of fungal origin / positive regulation of T-helper 17 type immune response / regulation of canonical NF-kappaB signal transduction / pattern recognition receptor activity / polysaccharide binding / phagocytosis, engulfment / stimulatory C-type lectin receptor signaling pathway / positive regulation of interleukin-10 production / positive regulation of phagocytosis / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / inflammatory response / external side of plasma membrane / innate immune response / cell surface / metal ion binding / plasma membrane
Similarity search - Function
C-type lectin domain family 7 member A / Natural killer cell receptor-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 ...C-type lectin domain family 7 member A / Natural killer cell receptor-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
C-type lectin domain family 7 member A
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrown, J. / O'Callaghan, C.A. / Marshall, A.S.J. / Gilbert, R.J.C. / Siebold, C. / Gordon, S. / Brown, G.D. / Jones, E.Y.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of the Fungal Beta-Glucan-Binding Immune Receptor Dectin-1: Implications for Function.
Authors: Brown, J. / O'Callaghan, C.A. / Marshall, A.S.J. / Gilbert, R.J.C. / Siebold, C. / Gordon, S. / Brown, G.D. / Jones, E.Y.
History
DepositionApr 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Mar 25, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DECTIN-1
B: DECTIN-1


Theoretical massNumber of molelcules
Total (without water)32,6582
Polymers32,6582
Non-polymers00
Water7,855436
1
A: DECTIN-1


Theoretical massNumber of molelcules
Total (without water)16,3291
Polymers16,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DECTIN-1


Theoretical massNumber of molelcules
Total (without water)16,3291
Polymers16,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.104, 57.104, 73.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 117 - 243 / Label seq-ID: 15 - 141

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.99887, 0.02025, -0.04306), (-0.0257, -0.99117, 0.13005), (-0.04005, 0.13101, 0.99057)
Vector: 0.29626, 27.30604, -1.90795)

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Components

#1: Protein DECTIN-1


Mass: 16329.065 Da / Num. of mol.: 2
Fragment: EXTRACELLULAR BETA-GLUCAN RECOGNITION DOMAIN, RESIDUES 113-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: RAW264.7 / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6QLQ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.42 %
Description: MOLECULAR REPLACEMENT USED THE CASPR WEBSERVER WITH 6 STARTING MODELS. STRUCTURAL ALIGNMENT OF STARTING MODELS WAS USED TO GENERATE HOMOLOGY MODELS AND POLY-ALA MODELS TO BE USED IN THE ...Description: MOLECULAR REPLACEMENT USED THE CASPR WEBSERVER WITH 6 STARTING MODELS. STRUCTURAL ALIGNMENT OF STARTING MODELS WAS USED TO GENERATE HOMOLOGY MODELS AND POLY-ALA MODELS TO BE USED IN THE MOLECULAR REPLACEMENT SEARCH.
Crystal growDetails: 0.2 M DI-AMMONIUM HYDROGEN CITRATE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 19, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 41593 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 78.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CaspRphasing
AMoREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87

1k9j

1fm5

1hq8

1ja3

1mpu

1e87


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.23 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1677 4 %RANDOM
Rwork0.214 ---
obs0.216 39882 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 0 436 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.8882958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97324.068118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.315352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8061510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021716
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21121
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21492
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8211.51294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27322052
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.98631038
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7934.5906
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1020 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal12
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 92
Rwork0.269 2318
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)
14.99871.4938-0.19921.3066-0.35441.86830.120.11560.29640.137-0.03540.0677-0.1194-0.0149-0.0846-0.19180.0150.0261-0.11190.0673-0.155813.43524.40737.833
23.90790.71860.50561.93750.49271.99850.1761-0.132-0.08330.1673-0.12210.02310.1559-0.0244-0.054-0.18860.0162-0.0027-0.1461-0.0142-0.2148-13.3487.54338.452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - 243
2X-RAY DIFFRACTION2B116 - 244

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