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- PDB-4c9f: Structure of SIGN-R1 in complex with Sulfodextran -

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Basic information

Entry
Database: PDB / ID: 4c9f
TitleStructure of SIGN-R1 in complex with Sulfodextran
ComponentsCD209 ANTIGEN-LIKE PROTEIN B
KeywordsMEMBRANE PROTEIN / C-TYPE LECTIN / INNATE IMMUNITY
Function / homology
Function and homology information


detection of yeast / (1->3)-beta-D-glucan binding / phagocytosis, recognition / D-mannose binding / polysaccharide binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production / external side of plasma membrane ...detection of yeast / (1->3)-beta-D-glucan binding / phagocytosis, recognition / D-mannose binding / polysaccharide binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production / external side of plasma membrane / membrane / metal ion binding
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
4-O-sulfo-alpha-D-glucopyranose / CD209 antigen-like protein B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSilva-Martin, N. / Bartual, S.G. / Rodriguez, A. / Ramirez, E. / Chacon, P. / Anthony, R.M. / Park, C.G. / Hermoso, J.A.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1
Authors: Silva-Martin, N. / Bartual, S.G. / Rodriguez, A. / Ramirez, E. / Chacon, P. / Anthony, R.M. / Park, C.G. / Hermoso, J.A.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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 16, 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: CD209 ANTIGEN-LIKE PROTEIN B
B: CD209 ANTIGEN-LIKE PROTEIN B
C: CD209 ANTIGEN-LIKE PROTEIN B
D: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,59124
Polymers62,0984
Non-polymers3,49320
Water2,954164
1
A: CD209 ANTIGEN-LIKE PROTEIN B
B: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,55012
Polymers31,0492
Non-polymers1,50110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-129.3 kcal/mol
Surface area12580 Å2
MethodPISA
2
C: CD209 ANTIGEN-LIKE PROTEIN B
D: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04112
Polymers31,0492
Non-polymers1,99210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-69.4 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.025, 97.959, 73.846
Angle α, β, γ (deg.)90.00, 120.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CD209 ANTIGEN-LIKE PROTEIN B / DC-SIGN-RELATED PROTEIN 1 / DC-SIGNR1 / OTB7 / SIGN-R1


Mass: 15524.574 Da / Num. of mol.: 4 / Fragment: CRD, RESIDUES 191-323 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: MACROPHAGES / References: UniProt: Q8CJ91

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 422.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcp[4S]a1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_4*OSO/3=O/3=O][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp4SO3]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 746.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcp[4S]a1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5_4*OSO/3=O/3=O][a2122h-1a_1-5]/1-2-2-2/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp4SO3]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-GQ1 / 4-O-sulfo-alpha-D-glucopyranose / 4-O-sulfo-alpha-D-glucose / 4-O-sulfo-D-glucose / 4-O-sulfo-glucose


Type: D-saccharide, alpha linking / Mass: 260.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O9S
IdentifierTypeProgram
DGlcp[4S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
4-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-Glcp4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 178 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.38 Å3/Da / Density % sol: 66.38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9334
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.58→61.8 Å / Num. obs: 30140 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.2
Reflection shellResolution: 2.58→2.98 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZHG

3zhg


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.36 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23265 1345 5 %RANDOM
Rwork0.19107 ---
obs0.19322 25612 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.518 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å2-1.02 Å2
2--1.8 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 201 164 4680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024643
X-RAY DIFFRACTIONr_bond_other_d0.0010.024134
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9636322
X-RAY DIFFRACTIONr_angle_other_deg0.9083.0079563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8835527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62225.094212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73515774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5811516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 105 -
Rwork0.275 1881 -
obs--98.81 %

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