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- PDB-2mk7: Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglyca... -

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Basic information

Entry
Database: PDB / ID: 2mk7
TitleTetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain
ComponentsAlpha-dystroglycan
KeywordsSTRUCTURAL PROTEIN / mucin domain / glycoprotein / glycosylation / alpha-dystroglycan / Tn antigen / N-acetyl-galactosamine
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / O-linked glycosylation ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / regulation of embryonic cell shape / retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / O-linked glycosylation / contractile ring / regulation of gastrulation / calcium-dependent cell-matrix adhesion / microtubule anchoring / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / basement membrane organization / positive regulation of myelination / regulation of epithelial to mesenchymal transition / dystroglycan binding / nerve development / cellular response to cholesterol / photoreceptor ribbon synapse / EGR2 and SOX10-mediated initiation of Schwann cell myelination / vinculin binding / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / costamere / skeletal muscle tissue regeneration / angiogenesis involved in wound healing / commissural neuron axon guidance / response to muscle activity / axon regeneration / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / structural constituent of muscle / positive regulation of cell-matrix adhesion / postsynaptic cytosol / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ECM proteoglycans / negative regulation of MAPK cascade / heart morphogenesis / GABA-ergic synapse / laminin binding / tubulin binding / SH2 domain binding / nuclear periphery / negative regulation of cell migration / filopodium / axon guidance / morphogenesis of an epithelium / adherens junction / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / Golgi lumen / Regulation of expression of SLITs and ROBOs / cellular response to mechanical stimulus / protein transport / lamellipodium / virus receptor activity / actin binding / basolateral plasma membrane / collagen-containing extracellular matrix / postsynaptic membrane / cytoskeleton / endoplasmic reticulum lumen / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / glutamatergic synapse / calcium ion binding / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain ...Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain / Cadherin-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Dystroglycan 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsLive, D. / Borgert, A.
CitationJournal: Glycobiology / Year: 2021
Title: Contrasting the conformational effects of alpha-O-GalNAc and alpha-O-Man glycan protein modifications and their impact on the mucin-like region of alpha-dystroglycan.
Authors: Borgert, A. / Foley, B.L. / Live, D.
History
DepositionFeb 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: 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_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8815
Polymers9961
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Alpha-dystroglycan / Alpha-DG / aDG


Mass: 996.180 Da / Num. of mol.: 1 / Fragment: mucin domain peptide (UNP residues 419-427) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14118
#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


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4 / 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Effects of O-GalNAc glycosylation on structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1223D TOCSY-NOESY
1322D 1H-15N HSQC
1422D 1H-13C HSQC
1522D 1H-1H TOCSY
1612D 1H-1H COSY
1722D 1H-13C HMBC

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Sample preparation

Details
Solution-IDContentsSolvent system
12-10 mM aDG mucin domain peptide, 100% D2O100% D2O
22-10 mM aDG mucin domain peptide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMaDG mucin domain peptide-12-101
mMaDG mucin domain peptide-22-102
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 softwareName: XPLOR-NIH / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: 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: 50 / Conformers submitted total number: 16

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