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- PDB-2mvk: Solution structure of phosphorylated cytosolic part of Trop2 -

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Basic information

Entry
Database: PDB / ID: 2mvk
TitleSolution structure of phosphorylated cytosolic part of Trop2
ComponentsTumor-associated calcium signal transducer 2
KeywordsSIGNALING PROTEIN / phospotilated cytosolic part of Trop2
Function / homology
Function and homology information


negative regulation of branching involved in ureteric bud morphogenesis / ureteric bud morphogenesis / negative regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of epithelial cell migration / positive regulation of stem cell differentiation / negative regulation of cell motility / regulation of epithelial cell proliferation / response to stimulus / negative regulation of stress fiber assembly ...negative regulation of branching involved in ureteric bud morphogenesis / ureteric bud morphogenesis / negative regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of epithelial cell migration / positive regulation of stem cell differentiation / negative regulation of cell motility / regulation of epithelial cell proliferation / response to stimulus / negative regulation of stress fiber assembly / lateral plasma membrane / visual perception / basal plasma membrane / extracellular space / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
Epithelial cell adhesion molecule N-terminal domain / Transmembrane glycoprotein EPCAM/Trop-2 / : / Epithelial cell adhesion molecule, N-terminal domain / EPCAM/Trop-2, C-terminal / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats.
Similarity search - Domain/homology
Tumor-associated calcium signal transducer 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsIlc, G. / Plavec, J. / Vidmar, T. / Pavsic, M. / Lenarcic, B.
CitationJournal: Sci Rep / Year: 2015
Title: The cytosolic tail of the tumor marker protein Trop2--a structural switch triggered by phosphorylation.
Authors: Pavsic, M. / Ilc, G. / Vidmar, T. / Plavec, J. / Lenarcic, B.
History
DepositionOct 8, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor-associated calcium signal transducer 2


Theoretical massNumber of molelcules
Total (without water)3,1771
Polymers3,1771
Non-polymers00
Water0
1


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

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Components

#1: Protein/peptide Tumor-associated calcium signal transducer 2 / Cell surface glycoprotein Trop-2 / Membrane component chromosome 1 surface marker 1 / Pancreatic ...Cell surface glycoprotein Trop-2 / Membrane component chromosome 1 surface marker 1 / Pancreatic carcinoma marker protein GA733-1


Mass: 3176.626 Da / Num. of mol.: 1 / Fragment: residues 298-323 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P09758

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 5mM Trop2ICP, trifluoroethanol/water / Solvent system: trifluoroethanol/water
SampleConc.: 5 mM / Component: Trop2ICP-1
Sample conditionsIonic strength: 0 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
YASARAKriegerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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