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- PDB-2cui: Solution structure of the 31st fibronectin type III domain of the... -

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Basic information

Entry
Database: PDB / ID: 2cui
TitleSolution structure of the 31st fibronectin type III domain of the human tenascin X
ComponentsTenascin-X
KeywordsCELL ADHESION / fibronectin type III domain / tenascin X precursor / extracellular matirx / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of cell fate determination / collagen fibril binding / positive regulation of collagen fibril organization / tenascin complex / elastic fiber assembly / positive regulation of vascular endothelial growth factor signaling pathway / collagen metabolic process / collagen fibril organization / extracellular matrix structural constituent / triglyceride metabolic process ...positive regulation of cell fate determination / collagen fibril binding / positive regulation of collagen fibril organization / tenascin complex / elastic fiber assembly / positive regulation of vascular endothelial growth factor signaling pathway / collagen metabolic process / collagen fibril organization / extracellular matrix structural constituent / triglyceride metabolic process / regulation of cell differentiation / ECM proteoglycans / regulation of cell adhesion / positive regulation of epithelial to mesenchymal transition / collagen binding / regulation of cell migration / extracellular matrix / cell-matrix adhesion / fatty acid metabolic process / cell-cell adhesion / neuron projection development / integrin binding / heparin binding / actin cytoskeleton organization / collagen-containing extracellular matrix / cell adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / : / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal ...Tenascin, EGF-like domain / Tenascin EGF domain / : / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsOhnishi, S. / Kigawa, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the 31st fibronectin type III domain of the human tenascin X
Authors: Ohnishi, S. / Kigawa, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2005Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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: Tenascin-X


Theoretical massNumber of molelcules
Total (without water)11,9271
Polymers11,9271
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)20 / 100target function, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Tenascin-X / TN-X / Hexabrachion-like protein


Mass: 11927.401 Da / Num. of mol.: 1 / Fragment: the 29th fibronectin type III domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TNXB / Plasmid: P050131-02 / References: UniProt: P22105

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.23mM protein U-15N, 13C; 20mM d-TrisHCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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