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- PDB-2hrl: Siglec-7 in complex with GT1b -

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Basic information

Entry
Database: PDB / ID: 2hrl
TitleSiglec-7 in complex with GT1b
ComponentsSialic acid-binding Ig-like lectin 7
KeywordsCELL ADHESION / Ig-like domain / Siglec / Ganglioside / Siglec-7
Function / homology
Function and homology information


sialic acid binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / carbohydrate binding / cell adhesion / plasma membrane
Similarity search - Function
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 ...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
ETHYL-TRIMETHYL-SILANE / Sialic acid-binding Ig-like lectin 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAttrill, H. / Imamura, A. / Sharma, R.S. / Kiso, M. / Crocker, P.R. / van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Siglec-7 Undergoes a Major Conformational Change When Complexed with the {alpha}(2,8)-Disialylganglioside GT1b
Authors: Attrill, H. / Imamura, A. / Sharma, R.S. / Kiso, M. / Crocker, P.R. / van Aalten, D.M.F.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Revision 2.1Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid-binding Ig-like lectin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1074
Polymers14,6551
Non-polymers1,4513
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.021, 46.021, 106.474
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 Sialic acid-binding Ig-like lectin 7 / Siglec-7 / QA79 membrane protein / Adhesion inhibitory receptor molecule 1 / AIRM-1 / p75 / D- ...Siglec-7 / QA79 membrane protein / Adhesion inhibitory receptor molecule 1 / AIRM-1 / p75 / D-siglec / CDw328 antigen


Mass: 14655.292 Da / Num. of mol.: 1
Fragment: Ig-like V-type, N-terminal domain, residues 18-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEF-Siglec-7 / Cell line (production host): CHO Lec1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9Y286
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta- ...N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1127.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-3[DGalpNAcb1-4]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-3-4/a4-b1_b3-c2_b4-e1_c8-d2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}[(4+1)][b-D-3-deoxy-GalpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CEQ / ETHYL-TRIMETHYL-SILANE


Mass: 102.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14Si
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM sodium acetate, 100mM sodium cacodylate, 30 % w/v PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. obs: 11626 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / Num. unique all: 11626 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O7V

1o7v


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.43 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23447 551 4.8 %RANDOM
Rwork0.19505 ---
all0.196 11626 --
obs0.19678 11045 99.35 %-
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: 24.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å2-0.48 Å20 Å2
2---0.96 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 96 60 1089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221095
X-RAY DIFFRACTIONr_angle_refined_deg1.4862.041508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6135124
X-RAY DIFFRACTIONr_chiral_restr0.0930.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02820
X-RAY DIFFRACTIONr_nbd_refined0.1890.2408
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.212
X-RAY DIFFRACTIONr_mcbond_it1.3313608
X-RAY DIFFRACTIONr_mcangle_it2.1123.2984
X-RAY DIFFRACTIONr_scbond_it2.0574487
X-RAY DIFFRACTIONr_scangle_it2.5733.5524
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 48
Rwork0.265 782

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