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- PDB-2acm: Solution structure of the SEA domain of human mucin 1 (MUC1) -

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Entry
Database: PDB / ID: 2acm
TitleSolution structure of the SEA domain of human mucin 1 (MUC1)
Components(Mucin-1) x 2
KeywordsSTRUCTURAL PROTEIN / auto-catalytic proteolysis
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Helix Hairpins - #600 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMacao, B. / Johansson, D.G.A. / Hansson, G.C. / Hard, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Autoproteolysis coupled to protein folding in the SEA domain of the membrane-bound MUC1 mucin
Authors: Macao, B. / Johansson, D.G.A. / Hansson, G.C. / Hard, T.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mucin-1
B: Mucin-1


Theoretical massNumber of molelcules
Total (without water)13,8792
Polymers13,8792
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with acceptable covalent geometry, structures with the least restraint violations
RepresentativeModel #1low energy

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Components

#1: Protein Mucin-1 / MUC1 mucus protein / MUC-1 / Polymorphic epithelial mucin / PEM / PEMT / Episialin / Tumor- ...MUC1 mucus protein / MUC-1 / Polymorphic epithelial mucin / PEM / PEMT / Episialin / Tumor-associated mucin / Carcinoma-associated mucin / Tumor-associated epithelial membrane antigen / EMA / H23AG / Peanut- reactive urinary mucin / PUM / Breast carcinoma-associated antigen DF3 / CD227 antigen


Mass: 7767.560 Da / Num. of mol.: 1 / Fragment: SEA domain (residues 1041-1097)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC1 / Plasmid: Pet3A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q16615, UniProt: P15941*PLUS
#2: Protein Mucin-1 / MUC1 mucus protein / MUC-1 / Polymorphic epithelial mucin / PEM / PEMT / Episialin / Tumor- ...MUC1 mucus protein / MUC-1 / Polymorphic epithelial mucin / PEM / PEMT / Episialin / Tumor-associated mucin / Carcinoma-associated mucin / Tumor-associated epithelial membrane antigen / EMA / H23AG / Peanut- reactive urinary mucin / PUM / Breast carcinoma-associated antigen DF3 / CD227 antigen


Mass: 6111.690 Da / Num. of mol.: 1 / Fragment: SEA domain (residues 1098-1152)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC1 / Plasmid: Pet3A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q16615, UniProt: P15941*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131CBCA(CO)NH
141HNCO

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Sample preparation

DetailsContents: 1mM SEA domain U-15N,13C; 20mM potassium phosphate, 20mM sodium chloride; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM KPi, 20mM NaCl / pH: 6.4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: XPLOR-NIH / Version: 2.1 / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Deposited coordinates are based on 1238 non-redundant NOE distance restraints, 180 dihedral angle restraints and 42 distance restraints for (21) hydrogen bonds
NMR representativeSelection criteria: low energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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