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- PDB-2lhw: Tri-O-GalNAc glycosylated Mucin sequence based on MUC2 Mucin glyc... -

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Basic information

Entry
Database: PDB / ID: 2lhw
TitleTri-O-GalNAc glycosylated Mucin sequence based on MUC2 Mucin glycoprotein tandem repeat
ComponentsMUC2 Mucin Domain Peptide
KeywordsSUGAR BINDING PROTEIN / glycosylation / Tn antigen
Function / homology2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion space simulated annealing
Model detailsclosest to the average, model 1
AuthorsBorgert, A. / Heimburg-Molinaro, J. / Lasanajak, Y. / Ju, T. / Liu, M. / Thompson, P. / Ragupathi, G. / Barany, G. / Cummings, R. / Smith, D. / Live, D.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Deciphering structural elements of mucin glycoprotein recognition.
Authors: Borgert, A. / Heimburg-Molinaro, J. / Song, X. / Lasanajak, Y. / Ju, T. / Liu, M. / Thompson, P. / Ragupathi, G. / Barany, G. / Smith, D.F. / Cummings, R.D. / Live, D.
History
DepositionAug 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nmr_ensemble / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_ensemble.conformer_selection_criteria / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 2.1Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MUC2 Mucin Domain Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4464
Polymers7821
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)39 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide MUC2 Mucin Domain Peptide


Mass: 781.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized via solid phase peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Compound detailsTHE MODIFIED SEQUENCE PTTTPLK FRAGMENT WAS CHOSEN BECAUSE IT WAS RELEVANT TO STRUCTURE/FUNCTION ...THE MODIFIED SEQUENCE PTTTPLK FRAGMENT WAS CHOSEN BECAUSE IT WAS RELEVANT TO STRUCTURE/FUNCTION ANALYSIS OF POST TRANSLATIONAL GLYCOSYLATION OF MUC2, FOR WHICH IT WAS USED AS A MODEL SUBSTRATE. STUDIES ON IT AND ON O-GALNAC GLYCOSYLATED FORMS HAD BEEN CARRIED OUT USING SEVERAL POLYPEPTIDE GALNAC TRANSFERASE ISOFORMS.
Sequence detailsTHE SEQUENCE PTTTP IS PART OF THE MUC2 MUCIN REPEAT POLYPEPTIDE PTTTPITTTTTVTPTPTPTGTQT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1213D TOCSY-NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1512D 1H-1H TOCSY
1622D 1H-1H COSY
1712D 1H-13C HMBC

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Sample preparation

Details
Solution-IDContentsSolvent system
12-10 mM MUC2 Mucin Domain Peptide, 2-10 mM SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE), 2-10 mM SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE), 2-10 mM SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE), 90% H2O/10% D2O90% H2O/10% D2O
22-10 mM MUC2 Mucin Domain Peptide, 2-10 mM SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE), 2-10 mM SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE), 2-10 mM SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE), 100% D2O100% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMMUC2 Mucin Domain Peptide-12-101
mMSUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)-22-101
mMSUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)-32-101
mMSUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)-42-101
mMMUC2 Mucin Domain Peptide-52-102
mMSUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)-62-102
mMSUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)-72-102
mMSUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)-82-102
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.structure solution
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion space simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 39 / Maximum distance constraint violation: 0.25 Å / Maximum torsion angle constraint violation: 5 °

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