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- PDB-2lvz: Solution structure of a Eosinophil Cationic Protein-trisaccharide... -

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Basic information

Entry
Database: PDB / ID: 2lvz
TitleSolution structure of a Eosinophil Cationic Protein-trisaccharide heparin mimetic complex
ComponentsEosinophil cationic protein
KeywordsHYDROLASE / heparin / molecular recognition
Function / homology
Function and homology information


induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen ...induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Eosinophil cationic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsGarcia Mayoral, M. / Canales, A. / Diaz, D. / Lopez Prados, J. / Moussaoui, M. / de Paz, J. / Angulo, J. / Nieto, P. / Jimenez Barbero, J. / Boix, E. / Bruix, M.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Insights into the glycosaminoglycan-mediated cytotoxic mechanism of eosinophil cationic protein revealed by NMR.
Authors: Garcia-Mayoral, M.F. / Canales, A. / Diaz, D. / Lopez-Prados, J. / Moussaoui, M. / de Paz, J.L. / Angulo, J. / Nieto, P.M. / Jimenez-Barbero, J. / Boix, E. / Bruix, M.
History
DepositionJul 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
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.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _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_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.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: Eosinophil cationic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5582
Polymers15,5991
Non-polymers9591
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Eosinophil cationic protein / ECP / Ribonuclease 3 / RNase 3


Mass: 15598.876 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE3, ECP, RNS3 / Production host: Escherichia coli (E. coli)
References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-propan-2-yl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside


Type: oligosaccharide / Mass: 958.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1a_1-5_1*OCC/3C_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][<C3>]{[(1+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-15N NOESY
1312D 1H-15N HSQC
1412D 1H-1H NOESY
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNCA
1813D HN(CO)CA
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] Eosinophil Cationic Protein, 0.5 mM Heparin (3-MER), 100 mM potassium phosphate, 300 mM potassium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMEosinophil Cationic Protein-1[U-13C; U-15N]1
0.5 mMHeparin (3-MER)-21
100 mMpotassium phosphate-31
300 mMpotassium chloride-41
Sample conditionsIonic strength: 0.3 / pH: 4.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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