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- PDB-2n7b: Solution structure of the human Siglec-8 lectin domain in complex... -

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Basic information

Entry
Database: PDB / ID: 2n7b
TitleSolution structure of the human Siglec-8 lectin domain in complex with 6'sulfo sialyl Lewisx
ComponentsSialic acid-binding Ig-like lectin 8
KeywordsSTRUCTURAL PROTEIN / Sialic acid-binding immunoglobulin-like lectin 8 / Siglec8 / SAF-2 / I-type lectin / carbohydrate-binding receptor / carbohydrate recognition / protein-glycan complex / sulfated sialyl Lewis X
Function / homology
Function and homology information


sialic acid binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / carbohydrate binding / cell adhesion / signal transduction / membrane / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3-aminopropan-1-ol / Sialic acid-binding Ig-like lectin 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsProepster, J.M. / Yang, F. / Rabbani, S. / Ernst, B. / Allain, F.H.-T. / Schubert, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8.
Authors: Propster, J.M. / Yang, F. / Rabbani, S. / Ernst, B. / Allain, F.H. / Schubert, M.
History
DepositionSep 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Oct 12, 2016Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid-binding Ig-like lectin 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6413
Polymers16,6651
Non-polymers9762
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sialic acid-binding Ig-like lectin 8 / Siglec-8 / Sialoadhesin family member 2 / SAF-2


Mass: 16665.463 Da / Num. of mol.: 1 / Fragment: N-terminal lectin domain (UNP residues 17-155) / Mutation: C26S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC8, SAF2 / Variant: SIGLEC8 / Plasmid: pET-43.1a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) / References: UniProt: Q9NYZ4
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-6-O-sulfo-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose- ...N-acetyl-alpha-neuraminic acid-(2-3)-6-O-sulfo-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 900.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalp[6S]b1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5_6*OSO/3=O/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp6SO3]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-0D8 / 3-aminopropan-1-ol


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1423D HNCA
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D HNCO
1823D HN(CO)CA
1933D (H)CCH-TOCSY
11023D 1H-15N NOESY
11142D 1H-1H NOESY
11223D 1H-13C NOESY aliphatic
11323D 1H-13C NOESY aromatic
11442D 1H-1H TOCSY
11532D 13C F2-filtered NOESY
11632D 13C F1-filtered TOCSY
11722D 13C F1-filtered TOCSY
21832D 13C F1-filtered F2-filtered NOESY
21933D 13C F1-edited F3-filtered NOESY
22012D 13C/15N F2-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.2 mM [U-100% 15N] Siglec, 20 mM potassium phosphate, 40 mM sodium chloride, 0.7-2.4 mM SUGAR (5-MER), 95% H2O/5% D2O95% H2O/5% D2O
20.3-1.2 mM [U-100% 13C; U-100% 15N] Siglec, 20 mM potassium phosphate, 40 mM sodium chloride, 0.7-2.4 mM SUGAR (5-MER), 95% H2O/5% D2O95% H2O/5% D2O
30.3-1.2 mM [U-100% 13C; U-100% 15N] Siglec, 20 mM potassium phosphate, 40 mM sodium chloride, 0.7-2.4 mM SUGAR (5-MER), 100% D2O100% D2O
40.3-1.2 mM [U-100% 15N] Siglec, 20 mM potassium phosphate, 40 mM sodium chloride, 0.7-2.4 mM SUGAR (5-MER), 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSiglec-8-1[U-100% 15N]0.7-1.21
20 mMpotassium phosphate-21
40 mMsodium chloride-31
mMSUGAR (5-MER)-40.7-2.41
mMSiglec-8-5[U-100% 13C; U-100% 15N]0.3-1.22
20 mMpotassium phosphate-62
40 mMsodium chloride-72
mMSUGAR (5-MER)-80.7-2.42
mMSiglec-8-9[U-100% 13C; U-100% 15N]0.3-1.23
20 mMpotassium phosphate-103
40 mMsodium chloride-113
mMSUGAR (5-MER)-120.7-2.43
mMSiglec-8-13[U-100% 15N]0.3-1.24
20 mMpotassium phosphate-144
40 mMsodium chloride-154
mMSUGAR (5-MER)-160.7-2.44
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.092 7.4 ambient 293 K
20.092 7.4 ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE7504
Bruker AvanceBrukerAVANCE9005

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospindata analysis
TopSpin3Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
ATNOS/CANDID2.1Herrmann, Guntert and Wuthrichpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
TALOS+Cornilescu, Delaglio and Baxprotein backbone torsion angle prediction from nmr chemical shifts
ProcheckNMRv.3.5.4Laskowski and MacArthurvalidation
Amber12Case, D.A. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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