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- PDB-1sl6: Crystal Structure of a fragment of DC-SIGNR (containg the carbohy... -

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Basic information

Entry
Database: PDB / ID: 1sl6
TitleCrystal Structure of a fragment of DC-SIGNR (containg the carbohydrate recognition domain and two repeats of the neck) complexed with Lewis-x.
ComponentsC-type lectin DC-SIGNR
KeywordsSUGAR BINDING PROTEIN / DC-SIGNR / C-TYPE LECTIN
Function / homology
Function and homology information


cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / fucose binding / virion binding / leukocyte cell-cell adhesion / RSV-host interactions / antigen processing and presentation / D-mannose binding ...cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / fucose binding / virion binding / leukocyte cell-cell adhesion / RSV-host interactions / antigen processing and presentation / D-mannose binding / viral genome replication / peptide antigen binding / calcium-dependent protein binding / host cell / virus receptor activity / signaling receptor activity / carbohydrate binding / adaptive immune response / receptor-mediated endocytosis of virus by host cell / receptor-mediated virion attachment to host cell / intracellular signal transduction / symbiont entry into host cell / immune response / external side of plasma membrane / innate immune response / virion attachment to host cell / 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) / 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
Lewis X antigen, alpha anomer / : / C-type lectin domain family 4 member M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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: 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 / entity_name_com / 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_molecule_features / 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.occupancy / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
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: C-type lectin DC-SIGNR
B: C-type lectin DC-SIGNR
C: C-type lectin DC-SIGNR
D: C-type lectin DC-SIGNR
E: C-type lectin DC-SIGNR
F: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,56636
Polymers128,4276
Non-polymers4,13930
Water4,252236
1
A: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.750, 153.750, 128.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
C-type lectin DC-SIGNR


Mass: 21404.506 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: A fragment containing the CRD domain and two repeats from the neck domain
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): BL21/DE3 / Production host: Escherichia coli (E. coli) / References: GenBank: 12084795, UniProt: Q9H2X3*PLUS
#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis X antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-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.: 24 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.69 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 300, 0.2M NaCl, 0.1 Hepes pH=7.5. Protein solution: 10 mg/ml protein, 5mM CaCl2, 10 mM 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: 1.0781 Å
DetectorType: ADSC / Detector: CCD / Date: Jul 3, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 83241 / Num. obs: 80306 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.054
Reflection shellResolution: 2.25→2.33 Å / Rsym value: 0.322 / % possible all: 84.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→41.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3723247.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6102 8.4 %RANDOM
Rwork0.219 ---
obs0.219 73013 87.6 %-
all-80292 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8621 Å2 / ksol: 0.348332 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1--13.33 Å2-4.11 Å20 Å2
2---13.33 Å20 Å2
3---26.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.25→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8256 0 240 236 8732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 790 8.4 %
Rwork0.299 8666 -
obs--68.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM_NCARBOHYDRATE.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5WATER.TOP

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