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- PDB-1url: N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH GLYCOPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1url
TitleN-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH GLYCOPEPTIDE
Components
  • ALA-GLY-HIS-THR-TRP-GLY-HIA
  • SIALOADHESIN
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / LECTIN/IG-DOMAIN / SIALOADHESIN / OLIGOSACCHARIDE MIMICS / MOLECULAR MIMICRY / CELL ADHESION / LECTIN / IMMUNOGLOBULIN DOMAIN / SUGAR BINDING PROTEIN IMMUNE SYSTEM COMPLEX / SUGAR BINDING PROTEIN / IMMUNE SYSTEM / SUGAR BINDING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of T cell apoptotic process / virion binding / positive regulation of extrinsic apoptotic signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set 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
N-acetyl-alpha-neuraminic acid / Sialoadhesin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBukrinsky, J.T. / Hilaire, P.M.S. / Meldal, M. / Crocker, P.R. / Henriksen, A.
Citation
Journal: Biochim.Biophys.Acta / Year: 2004
Title: Complex of Sialoadhesin with a Glycopeptide Ligand
Authors: Bukrinsky, J.T. / Hilaire, P.M.S. / Meldal, M. / Crocker, P.R. / Henriksen, A.
#1: Journal: Mol.Cell / Year: 1998
Title: Crystal Structure of the N-Terminal Domain of Sialoadhesin in Complex with 3' Sialyllactose at 1.85 A Resolution.
Authors: May, A.P. / Robinson, R.C. / Vinson, M. / Crocker, P.R. / Jones, E.Y.
History
DepositionOct 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: SIALOADHESIN
B: ALA-GLY-HIS-THR-TRP-GLY-HIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2783
Polymers13,9692
Non-polymers3091
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.230, 78.460, 34.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

DetailsTHE ENTRY IS MARKED AS DIMERIC AS PEPTIDE CHAIN B IS IN COMPLEX WITH PROTEIN CHAIN A FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350.

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Components

#1: Protein SIALOADHESIN / SIALIC ACID BINDING IG-LIKE LECTIN-1 / SIGLEC-1


Mass: 13204.021 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 20-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PEE14 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q62230
#2: Protein/peptide ALA-GLY-HIS-THR-TRP-GLY-HIA


Mass: 764.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HIA IS A MODIFIED HISTIDINE, O-SIALIC ACID BOUND ON THR B 4
Source: (synth.) synthetic construct (others)
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOL_ID 1 IS MACROPHAGE-RESTRICTED ADHESION MOLECULE THAT MEDIATES SIALIC-ACID DEPENDENT BINDING TO ...MOL_ID 1 IS MACROPHAGE-RESTRICTED ADHESION MOLECULE THAT MEDIATES SIALIC-ACID DEPENDENT BINDING TO LYMPHOCYTES GRANULOCYTES, MONOCYTES, NATURAL KILLER CELLS, B-CELLS AND CD8 T-CELLS. COULD ALSO PLAY A ROLE IN HEMOPOIESIS

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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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growpH: 5.6 / Details: 30% PEG4000, 0.1 M NA-CITRATE, 0.2 M AMSO4 PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.192
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.192 Å / Relative weight: 1
ReflectionResolution: 2.4→28.7 Å / Num. obs: 4194 / % possible obs: 87.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.6 / % possible all: 73.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFO

1qfo


Resolution: 2.4→28.74 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 659043.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: CYS A 17 MAKES A DISULPHIDE BOND WITH A SYMMETRY RELATED MOLECULE
RfactorNum. reflection% reflectionSelection details
Rfree0.273 224 5.4 %RANDOM
Rwork0.225 ---
obs0.225 4168 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2074 Å2 / ksol: 0.366536 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1--10.17 Å20 Å20 Å2
2---6.77 Å20 Å2
3---16.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 20 18 1004
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it21.5
X-RAY DIFFRACTIONc_mcangle_it3.622
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 36 6 %
Rwork0.372 566 -
obs--77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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