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- PDB-2cl8: Dectin-1 in complex with beta-glucan -

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Basic information

Entry
Database: PDB / ID: 2cl8
TitleDectin-1 in complex with beta-glucan
ComponentsDECTIN-1
KeywordsRECEPTOR / CARBOHYDRATE / FUNGAL RECOGNITION / CTLD / DECTIN-1 / LAMINARIN / BETA-GLUCAN / C-TYPE LECTIN-LIKE DOMAIN
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 / antifungal innate immune response / positive regulation of interleukin-23 production / CLEC7A (Dectin-1) signaling ...(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 / antifungal innate immune response / positive regulation of interleukin-23 production / CLEC7A (Dectin-1) signaling / opsonin binding / leukocyte activation involved in immune response / positive regulation of stress-activated MAPK cascade / response to yeast / phagocytosis, recognition / positive regulation of cytokine production involved in immune response / cell surface pattern recognition receptor signaling pathway / cell activation / positive regulation of calcineurin-NFAT signaling cascade / cellular response to molecule of fungal origin / positive regulation of T-helper 17 type immune response / regulation of canonical NF-kappaB signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / phagocytosis, engulfment / pattern recognition receptor activity / stimulatory C-type lectin receptor signaling pathway / polysaccharide binding / positive regulation of interleukin-10 production / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / positive regulation of phagocytosis / cell-cell adhesion / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / inflammatory response / innate immune response / external side of plasma membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_biol / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.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.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_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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 / struct_ncs_dom_lim
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 / _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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
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)32,9189
Polymers32,1922
Non-polymers7267
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-6.2 kcal/mol
Surface area14020 Å2
MethodPQS
Unit cell
Length a, b, c (Å)83.998, 83.998, 117.404
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

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: 4 / Auth seq-ID: 117 - 244 / Label seq-ID: 5 - 132

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

NCS oper: (Code: given
Matrix: (-1, 0.00057, -0.00244), (-0.00057, -1, 0.00018), (-0.00244, 0.00018, 1)
Vector: -84.01132, -0.0157, -0.12458)

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Components

#1: Protein DECTIN-1


Mass: 16095.844 Da / Num. of mol.: 2 / Fragment: C-TYPE LECTIN-LIKE DOMAIN, RESIDUES 113-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6QLQ4
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 3.72 Å3/Da / Density % sol: 66.93 %
Crystal growpH: 4
Details: 2M SODIUM CHLORIDE, 0.1M CITRIC ACID PH4.0, pH 4.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 2005 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12244 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 31.4 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 18.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 30.7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BPE

2bpe


Resolution: 2.8→72.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.6 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 584 4.8 %RANDOM
Rwork0.191 ---
obs0.194 11634 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.26 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 40 11 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212226
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.8673026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94824.017117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14415345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.281159
X-RAY DIFFRACTIONr_chiral_restr0.1170.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021733
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.2995
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21516
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.51300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11922060
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32631079
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8074.5963
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: 1043 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.40.5
medium thermal0.492
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.56 39
Rwork0.422 808

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