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- PDB-8s03: NMR solution structure of the CysD2 domain of MUC2 -

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Basic information

Entry
Database: PDB / ID: 8s03
TitleNMR solution structure of the CysD2 domain of MUC2
ComponentsMucin-2
KeywordsSTRUCTURAL PROTEIN / colon / transglutaminase / isopeptide bond
Function / homology
Function and homology information


inner mucus layer / outer mucus layer / host-mediated regulation of intestinal microbiota composition / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / maintenance of gastrointestinal epithelium / mucus secretion ...inner mucus layer / outer mucus layer / host-mediated regulation of intestinal microbiota composition / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / maintenance of gastrointestinal epithelium / mucus secretion / detoxification of copper ion / cupric ion binding / Dectin-2 family / cuprous ion binding / extracellular matrix / Golgi lumen / collagen-containing extracellular matrix / extracellular space / plasma membrane
Similarity search - Function
WxxW domain / Mucin-2 protein WxxW repeating region / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. ...WxxW domain / Mucin-2 protein WxxW repeating region / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / ENERGY MINIMIZATION
AuthorsRecktenwald, C. / Karlsson, B.G. / Garcia-Bonnete, M.-J. / Katona, G. / Jensen, M. / Lymer, R. / Baeckstroem, M. / Johansson, M.E.V. / Hansson, G.C. / Trillo-Muyo, S.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Cell Rep / Year: 2024
Title: The structure of the second CysD domain of MUC2 and role in mucin organization by transglutaminase-based cross-linking.
Authors: Recktenwald, C.V. / Karlsson, G. / Garcia-Bonete, M.J. / Katona, G. / Jensen, M. / Lymer, R. / Backstrom, M. / Johansson, M.E.V. / Hansson, G.C. / Trillo-Muyo, S.
History
DepositionFeb 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2612
Polymers15,2211
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mucin-2 / / MUC-2 / Intestinal mucin-2


Mass: 15221.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC2, SMUC / Cell line (production host): Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells / References: UniProt: Q02817
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H NOESY
122anisotropic12D 1H-15N HSQC
132anisotropic12D 1H-13C HSQC
142anisotropic13D HNCA
152anisotropic13D HN(CO)CA
162anisotropic13D HN(CA)CB
172anisotropic23D (H)CCH-TOCSY
182anisotropic13D 1H-13C NOESY aliphatic
192anisotropic13D 1H-15N NOESY
1103anisotropic12D 1H-13C HSQC15

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.7 mM 1H cysD2, 90% H2O/10% D2O10 mM phosphate 100 mM NaCl pH 7.01H_sample90% H2O/10% D2O
solution20.3 mM [U-100% 13C; U-100% 15N] cysD2, 90% H2O/10% D2OU13C15N labeling 10 mM phosphate 100 mM NaCl pH 7.013C15N90% H2O/10% D2O
solution30.6 mM 15N Cysteine, 15N Valine cysD2, 90% H2O/10% D2OU13C15N labeling 10 mM phosphate 100 mM NaCl pH 7.0CysVal90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMcysD21H1
0.3 mMcysD2[U-100% 13C; U-100% 15N]2
0.6 mMcysD215N Cysteine, 15N Valine3
Sample conditionsIonic strength: 100 mM / Ionic strength err: 1 / Label: standard / pH: 7 / PH err: 0.05 / Pressure: Atmospheric pressure bar / Pressure err: 0.01 / Temperature: 318 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD90013 mm TCI probe
Bruker AVANCE III HDBrukerAVANCE III HD80023 mm TCI probe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpinBruker Biospinprocessing
YASARA2.5Yasaara inc.refinement
CYANA3Peter Guentertstructure calculation
RefinementMethod: ENERGY MINIMIZATION / Software ordinal: 4
Details: 6 CALCIUM BOND DISTANCES, 14 HYDROGEN BONDS, 5 DISULFIDE BONDS, YASARA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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