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- PDB-4zet: Blood dendritic cell antigen 2 (BDCA-2) complexed with GalGlcNAcMan -

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Basic information

Entry
Database: PDB / ID: 4zet
TitleBlood dendritic cell antigen 2 (BDCA-2) complexed with GalGlcNAcMan
ComponentsC-type lectin domain family 4 member C
KeywordsCarbohydrate-binding protein / C-type lectin
Function / homology
Function and homology information


antifungal innate immune response / Dectin-2 family / tertiary granule membrane / ficolin-1-rich granule membrane / secretory granule membrane / carbohydrate binding / adaptive immune response / external side of plasma membrane / Neutrophil degranulation / metal ion binding / plasma membrane
Similarity search - Function
: / CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / 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) ...: / CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / 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 4 member C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsJegouzo, S.A.F. / Feinberg, H. / Dungarwalla, T. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
Funding support United Kingdom, United States, 4items
OrganizationGrant numberCountry
Wellcome Trust093599 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR001209 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2.
Authors: Jegouzo, S.A. / Feinberg, H. / Dungarwalla, T. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: 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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type lectin domain family 4 member C
B: C-type lectin domain family 4 member C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4846
Polymers34,3132
Non-polymers1,1714
Water00
1
A: C-type lectin domain family 4 member C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7423
Polymers17,1561
Non-polymers5862
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-type lectin domain family 4 member C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7423
Polymers17,1561
Non-polymers5862
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.559, 67.645, 118.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein C-type lectin domain family 4 member C / Blood dendritic cell antigen 2 / BDCA-2 / C-type lectin superfamily member 7 / Dendritic lectin


Mass: 17156.270 Da / Num. of mol.: 2 / Fragment: UNP residues 67-213 / Mutation: S67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CLEC4C, BDCA2, CLECSF11, CLECSF7, DLEC, HECL, UNQ9361/PRO34150
Production host: Escherichia coli (E. coli) / References: UniProt: Q8WTT0
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2-3/a2-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: protein solution comprising 6.2 mg/ml BDCA-2, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl and 20 mM GalGlcNAcMan. The reservoir solution contained 0.2 NH4Cl and 20% polyethylene glycol 3.35K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→37.56 Å / Num. obs: 7094 / % possible obs: 99.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.61 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.074 / Net I/σ(I): 8.7 / Num. measured all: 37251 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.9-3.075.20.514.3564610810.8230.24297.4
8.69-37.564.60.09213.714153090.9850.04898.1

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.9→37.56 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 354 5 %
Rwork0.178 6708 -
obs0.182 7062 98.94 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.98 Å2 / Biso mean: 32.122 Å2 / Biso min: 8.38 Å2
Refinement stepCycle: final / Resolution: 2.9→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 76 0 2480
Biso mean--31.54 --
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132576
X-RAY DIFFRACTIONf_angle_d1.1783472
X-RAY DIFFRACTIONf_chiral_restr0.049372
X-RAY DIFFRACTIONf_plane_restr0.005434
X-RAY DIFFRACTIONf_dihedral_angle_d16.113942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.31480.34911120.23022145X-RAY DIFFRACTION98
3.3148-4.17540.28061180.16992228X-RAY DIFFRACTION99
4.1754-37.56210.21911240.16072335X-RAY DIFFRACTION99

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