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- PDB-1sl5: Crystal Structure of DC-SIGN carbohydrate recognition domain comp... -

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Basic information

Entry
Database: PDB / ID: 1sl5
TitleCrystal Structure of DC-SIGN carbohydrate recognition domain complexed with LNFP III (Dextra L504).
ComponentsmDC-SIGN1B type I isoform
KeywordsSUGAR BINDING PROTEIN / DC-SIGN / C-TYPE LECTIN
Function / homology
Function and homology information


B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation ...B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / RSV-host interactions / D-mannose binding / antigen processing and presentation / positive regulation of T cell proliferation / CD209 (DC-SIGN) signaling / viral genome replication / endocytosis / peptide antigen binding / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / intracellular signal transduction / symbiont entry into host cell / immune response / external side of plasma membrane / innate immune response / virion attachment to host cell / cell surface / extracellular region / membrane / metal ion binding / plasma membrane / cytoplasm
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuo, Y. / Feinberg, H. / Conroy, E. / Mitchell, D.A. / Alvarez, R. / Blixt, O. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR
Authors: Guo, Y. / Feinberg, H. / Conroy, E. / Mitchell, D.A. / Alvarez, R. / Blixt, O. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_label_asym_id / _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_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.value / _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.ptnr2_label_seq_id
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: mDC-SIGN1B type I isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9275
Polymers16,1311
Non-polymers7964
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.57, 55.37, 29.63
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 mDC-SIGN1B type I isoform


Mass: 16130.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): BL21/DE3 / Production host: Escherichia coli (E. coli) / References: GenBank: 15281089, UniProt: Q9NNX6*PLUS
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-1/a3-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.88 Å3/Da / Density % sol: 33.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M MgCl2, 0.1M Tris pH 8.5. Protein solution: 10 mg/ml protein, 5mM CaCl2, 10mM oligosaccharide., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0894 Å
DetectorType: ADSC / Detector: CCD / Date: Jun 22, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0894 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 13737 / Num. obs: 12903 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.6 Å2 / Rsym value: 0.053
Reflection shellResolution: 1.7→1.76 Å / % possible all: 88.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.02 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1015228.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 909 8.2 %RANDOM
Rwork0.179 ---
all-12014 --
obs-11105 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.3354 Å2 / ksol: 0.361226 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--4.92 Å20 Å2
3----4.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 50 192 1306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 144 8.4 %
Rwork0.24 1580 -
obs-1724 90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM_NWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMCARBOHYDRATE.TOP_NEW
X-RAY DIFFRACTION5ION.TOP

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