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- PDB-1o7v: High resolution structure of Siglec-7 -

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Basic information

Entry
Database: PDB / ID: 1o7v
TitleHigh resolution structure of Siglec-7
ComponentsSIALIC ACID BINDING IG-LIKE LECTIN 7
KeywordsCELL ADHESION / SIGLEC / IMMUNOLOGLOBULIN-LIKE FOLD / LECTIN / SIALIC ACID BINDING PROTEIN / IMMUNE SYSTEM
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 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-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sialic acid-binding Ig-like lectin 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlphey, M.S. / Attrill, H. / Crocker, P.R. / Van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: High resolution crystal structures of Siglec-7. Insights into ligand specificity in the Siglec family.
Authors: Alphey, M.S. / Attrill, H. / Crocker, P.R. / van Aalten, D.M.
History
DepositionNov 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Sep 11, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / database_PDB_caveat / entity / exptl_crystal_grow / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_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 / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIALIC ACID BINDING IG-LIKE LECTIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8902
Polymers14,6551
Non-polymers1,2351
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.049, 40.049, 140.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SIALIC ACID BINDING IG-LIKE LECTIN 7 / QA79 MEMBRANE PROTEIN / ALLELIC VARIANT AIRM-1B / P75 / AIRM / AIRM-1 / SIGLEC-7 / D-SIGLEC / ...QA79 MEMBRANE PROTEIN / ALLELIC VARIANT AIRM-1B / P75 / AIRM / AIRM-1 / SIGLEC-7 / D-SIGLEC / ADHESION INHIBITORY RECEPTOR MOLECULE-1


Mass: 14655.292 Da / Num. of mol.: 1 / Fragment: V-SET SIALIC ACID BINDING DOMAIN, RESIDUES 18-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PDEF / Cell line (production host): CHO LEC1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9Y286
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.731 Å3/Da / Density % sol: 27.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
225 mMTris-HCl1droppH8.0
30.2 Mammonium acetate1reservoir
40.1 Mtrisodium citrate1reservoirpH5.6
530 %PEG40001reservoir
60.2 Msodium acetate trihydrate1reservoir
70.1 Msodium cacodylate1reservoirpH6.5
830 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 29, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 9146 / % possible obs: 94.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.4 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 9206 / Num. measured all: 31409
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O7S

1o7s


Resolution: 1.9→24.25 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1412842.78 / Cross valid method: THROUGHOUT / σ(F): 0
Details: FULL N-LINKED GLYCAN STRUCTURE SEEN (HIGH MANNOSE STRUCTURE)
RfactorNum. reflection% reflectionSelection details
Rfree0.258 479 5.2 %RANDOM
Rwork0.21 ---
obs0.21 9146 94.5 %-
Displacement parametersBiso mean: 34.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2--2.79 Å20 Å2
3----5.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 83 86 1198
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.6971.5
X-RAY DIFFRACTIONc_mcangle_it2.7962
X-RAY DIFFRACTIONc_scbond_it2.2972
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 69 5.9 %
Rwork0.291 1034 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.007

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