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- PDB-5wt7: FAS1-IV domain of Human Periostin -

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Basic information

Entry
Database: PDB / ID: 5wt7
TitleFAS1-IV domain of Human Periostin
ComponentsPeriostin
KeywordsCELL ADHESION / Periostin / Integrin / Cancer / Chronic allergic inflammation disease
Function / homology
Function and homology information


bone regeneration / cellular response to vitamin K / negative regulation of substrate adhesion-dependent cell spreading / regulation of Notch signaling pathway / tissue development / regulation of systemic arterial blood pressure / cellular response to fibroblast growth factor stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / response to muscle activity / neuron projection extension ...bone regeneration / cellular response to vitamin K / negative regulation of substrate adhesion-dependent cell spreading / regulation of Notch signaling pathway / tissue development / regulation of systemic arterial blood pressure / cellular response to fibroblast growth factor stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / response to muscle activity / neuron projection extension / negative regulation of cell-matrix adhesion / positive regulation of smooth muscle cell migration / response to mechanical stimulus / cell adhesion molecule binding / cellular response to transforming growth factor beta stimulus / extracellular matrix organization / extracellular matrix / macroautophagy / trans-Golgi network / neuromuscular junction / response to estradiol / cellular response to tumor necrosis factor / heparin binding / collagen-containing extracellular matrix / response to hypoxia / cell adhesion / extracellular space / metal ion binding
Similarity search - Function
FAS1 domain / FAS1 domain / TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. ...FAS1 domain / FAS1 domain / TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsYun, H. / Lee, C.W.
Funding supportKorea, Democratic People's Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2013R1A1A2009419 to C.W.LKorea, Democratic People's Republic Of
CitationJournal: Biomol NMR Assign / Year: 2018
Title: 1H,13C, and 15N resonance assignments of FAS1-IV domain of human periostin, a component of extracellular matrix proteins.
Authors: Yun, H. / Kim, E.H. / Lee, C.W.
History
DepositionDec 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periostin


Theoretical massNumber of molelcules
Total (without water)15,7111
Polymers15,7111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8760 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Periostin / / PN / Osteoblast-specific factor 2 / OSF-2


Mass: 15711.108 Da / Num. of mol.: 1 / Fragment: FAS1-IV domain, UNP residues 496-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POSTN, OSF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15063

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
213isotropic22D 1H-15N HSQC
224isotropic33D (H)CCH-TOCSY
234isotropic33D (H)CCH-COSY
244isotropic33D CCH-TOCSY
254isotropic23D HNCA
284isotropic23D HN(CO)CA
274isotropic23D HN(CA)CB
264isotropic23D CBCA(CO)NH
294isotropic23D HNCO
1103isotropic13D 1H-15N NOESY-HSQC
1113isotropic13D 1H-15N TOCSY-HSQC
3125isotropic22D 1H-13C HSQC
3135isotropic23D 1H-13C NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution3524 uM [U-99% 15N] Fasciclin1-IV, 90% H2O/10% D2O10 mM Sodium phosphate, 50 mM Sodium chloride, 0.04% Sodium azide, 10 uM DSS15N FAS1-IV90% H2O/10% D2O
solution4587 uM [U-99% 13C; U-99% 15N] Fasciclin1-IV, 90% H2O/10% D2O10 mM Sodium phosphate, 50 mM Sodium chloride, 0.04% Sodium azide, 10 uM DSS13C and 15N FAS1-IV90% H2O/10% D2O
solution5587 uM [U-100% 13C] Fasciclin1-IV, 100% D2O10 mM Sodium phosphate, 50 mM Sodium chloride, 0.04% Sodium azide, 10 uM DSS13C and 15N FAS1-IV100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
524 uMFasciclin1-IV[U-99% 15N]3
587 uMFasciclin1-IV[U-99% 13C; U-99% 15N]4
587 uMFasciclin1-IV[U-100% 13C]5
Sample conditions
Conditions-IDIonic strength unitsLabelpHPressure (kPa)Temperature (K)Details
1Not defined15N FAS1-IV7.0 ambient atm288 K
2Not defined13C and 15N FAS1-IV7.0 ambient atm288 K
3Not defined13C and 15N FAS1-IV7.0 ambient atm288 K100% D2O

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8003
Bruker AVANCE IIBrukerAVANCE II9002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 23

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