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- PDB-4zes: Blood dendritic cell antigen 2 (BDCA-2) complexed with methyl-man... -

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Basic information

Entry
Database: PDB / ID: 4zes
TitleBlood dendritic cell antigen 2 (BDCA-2) complexed with methyl-mannoside
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) / C-type lectin-like/link domain superfamily ...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
methyl alpha-D-mannopyranoside / C-type lectin domain family 4 member C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)34,8308
Polymers34,3132
Non-polymers5176
Water7,638424
1
A: C-type lectin domain family 4 member C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3913
Polymers17,1561
Non-polymers2342
Water181
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)17,4395
Polymers17,1561
Non-polymers2834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.713, 69.576, 117.506
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: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: protein solution comprising 5 mg/ml BDCA-2, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl and 50 mM methyl mannoside. The reservoir solution contained 0.2 M MgCl2, 20% polyethylene glycol 3.35K, mannoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.65→28.88 Å / Num. obs: 38138 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Net I/σ(I): 17.5 / Num. measured all: 243418
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
1.65-1.684.90.6032.5868817820.7490.29496.5
9.03-28.885.50.0343.515512840.9990.01496.8

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXdev_1760refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.65→28.88 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 -5 %
Rwork0.1733 36178 -
obs0.1753 38083 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.73 Å2 / Biso mean: 26.0717 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 1.65→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 53 414 2871
Biso mean--27.83 34.02 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112598
X-RAY DIFFRACTIONf_angle_d1.0253509
X-RAY DIFFRACTIONf_chiral_restr0.046366
X-RAY DIFFRACTIONf_plane_restr0.005443
X-RAY DIFFRACTIONf_dihedral_angle_d13.089950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69030.28221300.23622472X-RAY DIFFRACTION98
1.6903-1.7360.2881350.21662557X-RAY DIFFRACTION100
1.736-1.78710.2971330.21192544X-RAY DIFFRACTION100
1.7871-1.84480.23321340.19352551X-RAY DIFFRACTION100
1.8448-1.91070.22771340.18452539X-RAY DIFFRACTION100
1.9107-1.98720.21931370.18092591X-RAY DIFFRACTION100
1.9872-2.07760.20211340.17742542X-RAY DIFFRACTION100
2.0776-2.18710.231350.17612578X-RAY DIFFRACTION100
2.1871-2.32410.20851360.16982584X-RAY DIFFRACTION100
2.3241-2.50340.2081360.18062584X-RAY DIFFRACTION100
2.5034-2.75520.24321360.18712589X-RAY DIFFRACTION100
2.7552-3.15340.22891390.18012631X-RAY DIFFRACTION100
3.1534-3.97130.20981380.15692634X-RAY DIFFRACTION100
3.9713-28.87950.17021480.15162782X-RAY DIFFRACTION100

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