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

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Basic information

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


(1->3)-beta-D-glucan immune receptor activity / detection of yeast / detection of molecule of fungal origin / (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 / antifungal innate immune response / opsonin binding ...(1->3)-beta-D-glucan immune receptor activity / detection of yeast / detection of molecule of fungal origin / (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 / antifungal innate immune response / opsonin binding / 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 calcium-mediated signaling / positive regulation of interleukin-2 production / cell-cell adhesion / positive regulation of DNA-binding transcription factor activity / 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: 2.25 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 31, 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,06510
Polymers32,4542
Non-polymers6108
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-10.5 kcal/mol
Surface area14980 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.685, 84.685, 117.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEUAA117 - 2446 - 133
21GLNGLNLEULEUBB117 - 2446 - 133
12PG4PG4PG4PG4AF1248
22PG4PG4PG4PG4BJ1248

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-1, 0.00063, 0.001), (-0.00063, -1, 0.00092), (0.001, 0.00092, 1)
Vector: 42.29076, 73.35347, -0.05533)

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Components

#1: Protein DECTIN-1


Mass: 16227.040 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.77 Å3/Da / Density % sol: 67.36 %
Description: IN ADDITION TO THIS MODEL, CASPR GENERATED HOMOLOGY MODELS AND TRUNCATED MODELS TO USE IN MOLECULAR REPLACEMENT SEARCH
Crystal growpH: 4.6
Details: 2M SODIUM CHLORIDE, 0.1M SODIUM ACETATE PH4.6, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2004 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 22768 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / % possible all: 76.9

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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 ENTRY 2BPD

2bpd


Resolution: 2.25→73.32 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.791 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1165 5.1 %RANDOM
Rwork0.188 ---
obs0.19 21569 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 30 200 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212206
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9012984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7465254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7724.237118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35315344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.141158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21458
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.2110
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.861.51305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52322054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9731061
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0244.5930
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1054medium positional0.360.5
12B1054medium positional0.360.5
21A12medium positional0.070.5
22B12medium positional0.070.5
11A1054medium thermal0.442
12B1054medium thermal0.442
21A12medium thermal0.392
22B12medium thermal0.392
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 69
Rwork0.263 1211
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)
13.3625-0.3838-0.75271.5014-0.86953.0015-0.1408-0.1482-0.56330.14450.40420.62180.2878-0.8934-0.26350.0421-0.03470.06530.26010.18710.151315.12325.11237.516
23.451-0.09990.6421.42111.04423.3650.0142-0.0357-0.06190.08190.0674-0.1090.01030.0492-0.0816-0.02690.03660.0086-0.0591-0.0101-0.14139.37240.28531.289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - 245
2X-RAY DIFFRACTION2B117 - 244

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