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- PDB-5b1x: Crystal structure of human dendritic cell inhibitory receptor (DC... -

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Basic information

Entry
Database: PDB / ID: 5b1x
TitleCrystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in complex with biantennary glycan
ComponentsC-type lectin domain family 4 member A
KeywordsCARBOHYDRATE BINDING PROTEIN / C-type lectin / innate immunity / carbohydrate recognition
Function / homology
Function and homology information


plasmacytoid dendritic cell antigen processing and presentation / antifungal innate immune response / CD8-positive, alpha-beta T cell activation / negative regulation of cytokine production / pattern recognition receptor activity / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / D-mannose binding / negative regulation of tumor necrosis factor production / transmembrane signaling receptor activity ...plasmacytoid dendritic cell antigen processing and presentation / antifungal innate immune response / CD8-positive, alpha-beta T cell activation / negative regulation of cytokine production / pattern recognition receptor activity / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / D-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) ...: / 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: 2.902 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: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _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.pdbx_value_order / _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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 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)65,10416
Polymers63,2504
Non-polymers1,85412
Water36020
1
A: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2764
Polymers15,8121
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area7460 Å2
MethodPISA
2
B: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2764
Polymers15,8121
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area7460 Å2
MethodPISA
3
C: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2764
Polymers15,8121
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area7480 Å2
MethodPISA
4
D: C-type lectin domain family 4 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2764
Polymers15,8121
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.669, 104.845, 65.354
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 106-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4A, CLECSF6, DCIR, LLIR, HDCGC13P / Plasmid: pCold / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9UMR7
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M potassium thiocyanate and 20%(w/v) polyethylene glycol monomethyl ether 2,000

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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: Dec 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 16219 / % possible obs: 100 % / Redundancy: 6.6 % / Rsym value: 0.167 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.5 / % 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: 2.902→46.689 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.29 813 5.03 %Random selection
Rwork0.2599 ---
obs0.2615 16149 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.902→46.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 112 20 4434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134614
X-RAY DIFFRACTIONf_angle_d0.6126194
X-RAY DIFFRACTIONf_dihedral_angle_d14.6182734
X-RAY DIFFRACTIONf_chiral_restr0.042618
X-RAY DIFFRACTIONf_plane_restr0.004806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9017-3.08340.34291400.31332495X-RAY DIFFRACTION99
3.0834-3.32150.32971410.29642499X-RAY DIFFRACTION100
3.3215-3.65560.31331190.26562546X-RAY DIFFRACTION100
3.6556-4.18430.28391550.24192515X-RAY DIFFRACTION100
4.1843-5.27060.24511400.22392571X-RAY DIFFRACTION100
5.2706-46.69460.25141180.25092710X-RAY DIFFRACTION99

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