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- PDB-3wbp: Crystal structure of carbohydrate recognition domain of Blood Den... -

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Basic information

Entry
Database: PDB / ID: 3wbp
TitleCrystal structure of carbohydrate recognition domain of Blood Dendritic Cell Antigen-2 (BDCA2) lectin (crystal form-1)
ComponentsC-type lectin domain family 4 member C
KeywordsCarbohydrate Binding Protein / C-type lectin fold / immune receptor / complex-type N-glycan
Function / homology
Function and homology information


antifungal innate immune response / pattern recognition receptor activity / 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 ...antifungal innate immune response / pattern recognition receptor activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNagae, M. / Ikeda, A. / Kitago, Y. / Matsumoto, N. / Yamamoto, K. / Yamaguchi, Y.
CitationJournal: Proteins / Year: 2014
Title: Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer.
Authors: Nagae, M. / Ikeda, A. / Kitago, Y. / Matsumoto, N. / Yamamoto, K. / Yamaguchi, Y.
History
DepositionMay 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)36,3034
Polymers36,1782
Non-polymers1242
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.115, 82.115, 44.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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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: 18089.225 Da / Num. of mol.: 2 / Fragment: UNP residues 83-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BDCA2 / Plasmid: pCold-TEV vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q8WTT0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 1.5M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 27881 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.039 / Net I/σ(I): 56.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3VYJ

3vyj


Resolution: 1.8→82.11 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.488 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27219 1403 5 %RANDOM
Rwork0.25422 ---
obs0.25512 26467 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.388 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0 Å20 Å2
2---1.33 Å2-0 Å2
3---2.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→82.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 8 24 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022164
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.8942932
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.725251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39324.286112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5151512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211672
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 101 -
Rwork0.291 1865 -
obs--99.9 %

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