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- PDB-2v37: Solution structure of the N-terminal extracellular domain of huma... -

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Basic information

Entry
Database: PDB / ID: 2v37
TitleSolution structure of the N-terminal extracellular domain of human T- cadherin
ComponentsCADHERIN-13
KeywordsCELL ADHESION / LIPOPROTEIN / POLYMORPHISM / GLYCOPROTEIN / ADIPONECTIN RECEPTOR / EXTRACELLULAR PROTEIN / CALCIUM / MEMBRANE / T-CADHERIN / GPI-ANCHOR / CLASSICAL CADHERIN / CELL-CELL ADHESION / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


low-density lipoprotein particle mediated signaling / adiponectin binding / regulation of epidermal growth factor receptor signaling pathway / : / localization within membrane / low-density lipoprotein particle binding / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of cell adhesion / Adherens junctions interactions ...low-density lipoprotein particle mediated signaling / adiponectin binding / regulation of epidermal growth factor receptor signaling pathway / : / localization within membrane / low-density lipoprotein particle binding / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of cell adhesion / Adherens junctions interactions / catenin complex / adherens junction organization / sprouting angiogenesis / positive regulation of positive chemotaxis / lamellipodium assembly / positive regulation of cell-matrix adhesion / Rac protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / lipoprotein particle binding / Rho protein signal transduction / regulation of endocytosis / keratinocyte proliferation / endothelial cell migration / positive regulation of calcium-mediated signaling / positive regulation of endothelial cell proliferation / caveola / positive regulation of smooth muscle cell proliferation / mitotic cell cycle / collagen-containing extracellular matrix / neuron projection / positive regulation of cell migration / cadherin binding / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Cadherin-13 / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Cadherin-13 / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / X-PLOR-NIH
AuthorsDames, S.A. / Bang, E.J. / Ahrens, T. / Haeussinger, D. / Grzesiek, S.
CitationJournal: J. Biol. Chem. / Year: 2008
Title: Insights into the low adhesive capacity of human T-cadherin from the NMR structure of Its N-terminal extracellular domain.
Authors: Dames, S.A. / Bang, E. / Haussinger, D. / Ahrens, T. / Engel, J. / Grzesiek, S.
History
DepositionJun 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CADHERIN-13


Theoretical massNumber of molelcules
Total (without water)11,7551
Polymers11,7551
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 / 200LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein CADHERIN-13 / / HUMAN T-CADHERIN / TRUNCATED-CADHERIN / T-CADHERIN / T-CAD / HEART-CADHERIN / H-CADHERIN / P105


Mass: 11755.238 Da / Num. of mol.: 1 / Fragment: EC1, RESIDUES 139-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET19B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55290
Compound detailsCADHERINS ARE CALCIUM DEPENDENT CELL ADHESION PROTEINS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
221HN(CA)CB
331CBCA(CO)NH
441(H)CCH-TOCSY
551HNCO
66115N- AND 13C-EDITED NOESY
771HNCA
881HN(CA)CB
991CBCA(CO)NH
10101(H)CCH- TOCSY
11111HNCO
1212115N-
1313113C- EDITED NOESY
NMR detailsText: ASSIGNMENTS AND STRUCTURAL DATA WERE OBTAINED USING MULTDIMENSIONAL, MULTINUCLEAR NMR DATA OF 15N, 13C LABELED HUMAN T-CADHERIN 1-105. THE STRUCTURES WERE CALCULATED BY TORSION ANGLE DYNAMICS ...Text: ASSIGNMENTS AND STRUCTURAL DATA WERE OBTAINED USING MULTDIMENSIONAL, MULTINUCLEAR NMR DATA OF 15N, 13C LABELED HUMAN T-CADHERIN 1-105. THE STRUCTURES WERE CALCULATED BY TORSION ANGLE DYNAMICS FOLLOWED BY MOLECULAR DYNAMICS IN CARTESIAN SPACE. THE FINAL 20 STRUCTURES WERE FURTHER REFINED IN A WATER-SHELL.

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Sample preparation

DetailsContents: 5% H2O/ 95% D2O OR 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM7.8 1.0 atm298.0 K
210 mM7.8 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHBRUNGER, SCHWIETERS, CLORErefinement
NMRViewstructure solution
RefinementMethod: X-PLOR-NIH / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND UNDER EXPERIMENTAL DETAILS AND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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