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- PDB-1xph: Structure of DC-SIGNR and a portion of repeat domain 8 -

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Basic information

Entry
Database: PDB / ID: 1xph
TitleStructure of DC-SIGNR and a portion of repeat domain 8
ComponentsCD209 antigen-like protein 1
KeywordsIMMUNE SYSTEM / SUGAR BINDING PROTEIN / C-type lectin / carbohydrate recognition domain / repeat domain
Function / homology
Function and homology information


cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding ...cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / receptor-mediated endocytosis of virus by host cell / viral genome replication / peptide antigen binding / calcium-dependent protein binding / signaling receptor activity / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / receptor-mediated virion attachment to host cell / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / extracellular region / metal ion binding / membrane / 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
C-type lectin domain family 4 member M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsSnyder, G.A. / Colonna, M. / Sun, P.D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The structure of DC-SIGNR with a portion of its repeat domain lends insights to modeling of the receptor tetramer.
Authors: Snyder, G.A. / Colonna, M. / Sun, P.D.
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: CD209 antigen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,5631
Non-polymers401
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.233, 54.887, 62.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CD209 antigen-like protein 1 / Dendritic cell-specific ICAM-3 non-integrin related DC-SIGNR / Carbohydrate recognition domain and ...Dendritic cell-specific ICAM-3 non-integrin related DC-SIGNR / Carbohydrate recognition domain and repeat 8 of DC-SIGNR / Dendritic cell-specific ICAM-3-grabbing nonintegrin 2 / DC-SIGN2 / DC-SIGN related protein / DC-SIGNR / Liver/lymph node specific ICAM-3-grabbing nonintegrin / L-SIGN


Mass: 17563.219 Da / Num. of mol.: 1
Fragment: sequence database residues 250-399: contains C-type lectin domain (residues 274-390)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 (DE3) / References: UniProt: Q9H2X3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.8 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MgCl2, 100mM Na Cacodylate, 12% PEG 3000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0395 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0395 Å / Relative weight: 1
ReflectionResolution: 1.41→31.4 Å / Num. all: 25340 / Num. obs: 25340 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Rsym value: 0.069
Reflection shellResolution: 1.41→1.48 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.222 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K9J

1k9j


Resolution: 1.41→31.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.858 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19295 1290 5.1 %RANDOM
Rwork0.17613 ---
obs0.17698 23999 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.41→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 1 103 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211174
X-RAY DIFFRACTIONr_bond_other_d0.0030.02931
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.881591
X-RAY DIFFRACTIONr_angle_other_deg0.82832166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_nbd_refined0.3190.2256
X-RAY DIFFRACTIONr_nbd_other0.250.21149
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.2618
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3670.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9641.5689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79521100
X-RAY DIFFRACTIONr_scbond_it2.4913485
X-RAY DIFFRACTIONr_scangle_it3.9754.5491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.448 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.197 113
Rwork0.192 1759

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