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- PDB-5b1w: Crystal structure of human dendritic cell inhibitory receptor (DC... -

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Basic information

Entry
Database: PDB / ID: 5b1w
TitleCrystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form
ComponentsC-type lectin domain family 4 member A
KeywordsCARBOHYDRATE BINDING PROTEIN / C-type lectin domain / innate immunity / carbohydrate recognition
Function / homology
Function and homology information


plasmacytoid dendritic cell antigen processing and presentation / antifungal innate immune response / negative regulation of cytokine production / CD8-positive, alpha-beta T cell activation / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / mannose binding / negative regulation of tumor necrosis factor production / transmembrane signaling receptor activity / carbohydrate binding ...plasmacytoid dendritic cell antigen processing and presentation / antifungal innate immune response / negative regulation of cytokine production / CD8-positive, alpha-beta T cell activation / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / mannose binding / negative regulation of tumor necrosis factor production / transmembrane signaling receptor activity / carbohydrate binding / adaptive immune response / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / calcium 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
C-type lectin domain family 4 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsNagae, M. / Yamaguchi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT24770111 Japan
MEXT15K18496 Japan
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan
Authors: Nagae, M. / Ikeda, A. / Hanashima, S. / Kojima, T. / Matsumoto, N. / Yamamoto, K. / Yamaguchi, Y.
History
DepositionDec 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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


Theoretical massNumber of molelcules
Total (without water)63,57112
Polymers63,2504
Non-polymers3218
Water1267
1
A: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8933
Polymers15,8121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area7540 Å2
MethodPISA
2
B: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8933
Polymers15,8121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area7710 Å2
MethodPISA
3
C: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8933
Polymers15,8121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area7310 Å2
MethodPISA
4
D: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8933
Polymers15,8121
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.489, 105.832, 65.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
C-type lectin domain family 4 member A / C-type lectin DDB27 / C-type lectin superfamily member 6 / Dendritic cell immunoreceptor / Lectin- ...C-type lectin DDB27 / C-type lectin superfamily member 6 / Dendritic cell immunoreceptor / Lectin-like immunoreceptor


Mass: 15812.479 Da / Num. of mol.: 4 / Fragment: UNP residues 106-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4A, CLECSF6, DCIR, LLIR, HDCGC13P / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9UMR7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl (pH 8.5), 0.2M sodium acetate and 30%(w/v) polyethylene glycol 4,000

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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 270 / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.05→100 Å / Num. obs: 14032 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rsym value: 0.173 / Net I/σ(I): 9
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYK

3vyk


Resolution: 3.05→47.019 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2845 684 4.9 %Random selection
Rwork0.2525 ---
obs0.2541 13961 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→47.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 0 8 7 4301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114492
X-RAY DIFFRACTIONf_angle_d0.6166030
X-RAY DIFFRACTIONf_dihedral_angle_d12.5882654
X-RAY DIFFRACTIONf_chiral_restr0.043580
X-RAY DIFFRACTIONf_plane_restr0.004800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.28430.34031290.31982574X-RAY DIFFRACTION97
3.2843-3.61470.32531380.27882615X-RAY DIFFRACTION100
3.6147-4.13750.29771310.24622653X-RAY DIFFRACTION100
4.1375-5.21170.23811380.21882661X-RAY DIFFRACTION99
5.2117-47.02440.24961480.22512774X-RAY DIFFRACTION98

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