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

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Basic information

Entry
Database: PDB / ID: 2bph
TitleSTRUCTURE OF MURINE DECTIN-1
ComponentsDECTIN-1CLEC7A
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 / positive regulation of lymphocyte activation / detection of yeast / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / cell recognition / detection of fungus / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production ...(1->3)-beta-D-glucan immune receptor activity / positive regulation of lymphocyte activation / detection of yeast / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / cell recognition / detection of fungus / 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 / positive regulation of cell maturation / positive regulation of cytokine production involved in immune response / antifungal innate immune response / opsonin binding / positive regulation of interleukin-23 production / positive regulation of stress-activated MAPK cascade / CLEC7A (Dectin-1) signaling / response to yeast / leukocyte activation involved in immune response / cell activation / phagocytosis, recognition / positive regulation of killing of cells of another organism / cellular response to molecule of fungal origin / positive regulation of T-helper 17 type immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of monocyte chemotactic protein-1 production / regulation of canonical NF-kappaB signal transduction / pattern recognition receptor activity / phagocytosis, engulfment / polysaccharide binding / positive regulation of wound healing / positive regulation of respiratory burst / stimulatory C-type lectin receptor signaling pathway / positive regulation of interleukin-10 production / positive regulation of calcium-mediated signaling / positive regulation of phagocytosis / positive regulation of interleukin-2 production / positive regulation of interleukin-12 production / positive regulation of superoxide anion generation / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of protein-containing complex assembly / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / inflammatory response / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / cell surface / identical protein binding / metal ion binding / plasma membrane / cytoplasm
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: 2.2 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 1.2Apr 3, 2019Group: Data collection / Other / Category: pdbx_database_proc / pdbx_database_status / Item: _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)32,5034
Polymers32,4542
Non-polymers492
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-11.3 kcal/mol
Surface area15590 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.199, 57.199, 72.996
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: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 117 - 244 / Label seq-ID: 6 - 133

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

NCS oper: (Code: given
Matrix: (-0.99869, 0.01789, 0.04796), (-0.02451, -0.98967, -0.14122), (0.04494, -0.14221, 0.98882)
Vector: 55.69507, 72.34037, 3.7809)

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Components

#1: Protein DECTIN-1 / CLEC7A


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 (E. coli) / Variant (production host): Rosetta / References: UniProt: Q6QLQ4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growpH: 6.5
Details: 0.2 M POTASSIUM CHLORIDE, 0.05M SODIUM CACODYLATE PH6.5, 0.1M MAGNESIUM ACETATE, 10% PEG 8000, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 13478 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BPD

2bpd


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.208 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 666 4.9 %RANDOM
Rwork0.195 ---
obs0.198 12791 99.8 %-
Displacement parametersBiso mean: 33.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 2 170 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.892930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86624.211114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.196158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21041
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21416
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5591.51304
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94722042
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57131014
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2394.5888
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 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
512medium positional0.190.5
531loose positional0.585
512medium thermal0.752
531loose thermal1.3510
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 57
Rwork0.252 925
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)
18.41311.93090.3312.1470.67532.58710.1365-0.0143-0.30570.1608-0.03550.00420.26990.0562-0.101-0.13940.0406-0.0299-0.0349-0.0849-0.165315.12325.11237.516
25.08190.8506-0.39932.614-0.3672.8090.2381-0.15210.08670.183-0.1219-0.1072-0.17090.1303-0.1161-0.12220.0397-0.0014-0.10480.0284-0.198442.86741.80938.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - 244
2X-RAY DIFFRACTION2B117 - 244

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