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- PDB-2k8p: Characterisation of the structural features and interactions of s... -

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Basic information

Entry
Database: PDB / ID: 2k8p
TitleCharacterisation of the structural features and interactions of sclerostin: molecular insight into a key regulator of Wnt-mediated bone formation
ComponentsSclerostin
KeywordsSIGNALING PROTEIN / WNT SIGNALLING PATHWAY / BONE FORMATION / Alternative splicing / Glycoprotein / Secreted
Function / homology
Function and homology information


Negative regulation of TCF-dependent signaling by WNT ligand antagonists / BMP binding / negative regulation of ossification / cellular response to parathyroid hormone stimulus / negative regulation of Wnt signaling pathway / molecular function inhibitor activity / negative regulation of BMP signaling pathway / canonical Wnt signaling pathway / localization / negative regulation of protein-containing complex assembly ...Negative regulation of TCF-dependent signaling by WNT ligand antagonists / BMP binding / negative regulation of ossification / cellular response to parathyroid hormone stimulus / negative regulation of Wnt signaling pathway / molecular function inhibitor activity / negative regulation of BMP signaling pathway / canonical Wnt signaling pathway / localization / negative regulation of protein-containing complex assembly / BMP signaling pathway / response to mechanical stimulus / ossification / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / heparin binding / carbohydrate binding / DNA-binding transcription factor binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
Sclerostin/Sclerostin domain-containing protein 1 / Sclerostin (SOST) / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine-knot cytokine
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVeverka, V. / Henry, A.J. / Slocombe, P.M. / Ventom, A. / Mulloy, B. / Muskett, F.W. / Muzylak, M. / Greenslade, K. / Moore, A. / Zhang, L. ...Veverka, V. / Henry, A.J. / Slocombe, P.M. / Ventom, A. / Mulloy, B. / Muskett, F.W. / Muzylak, M. / Greenslade, K. / Moore, A. / Zhang, L. / Gong, J. / Qian, X. / Paszty, C. / Taylor, R.J. / Robinson, M.K. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Characterization of the Structural Features and Interactions of Sclerostin: Molecular insight into a key regulator of Wnt-mediated bone formation
Authors: Veverka, V. / Henry, A.J. / Slocombe, P.M. / Ventom, A. / Mulloy, B. / Muskett, F.W. / Muzylak, M. / Greenslade, K. / Moore, A. / Zhang, L. / Gong, J. / Qian, X. / Paszty, C. / Taylor, R.J. ...Authors: Veverka, V. / Henry, A.J. / Slocombe, P.M. / Ventom, A. / Mulloy, B. / Muskett, F.W. / Muzylak, M. / Greenslade, K. / Moore, A. / Zhang, L. / Gong, J. / Qian, X. / Paszty, C. / Taylor, R.J. / Robinson, M.K. / Carr, M.D.
History
DepositionSep 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sclerostin


Theoretical massNumber of molelcules
Total (without water)21,4321
Polymers21,4321
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)36 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Sclerostin /


Mass: 21432.332 Da / Num. of mol.: 1 / Fragment: UNP residues 25 to 213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOST, UNQ2976/PRO7455/PRO7476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQB4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1533D CBCA(CO)NH
1633D HN(CA)CB
1733D (H)CCH-TOCSY
1823D 1H-13C NOESY
1933D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1310 uM entity, 5 % D2O, 95 % H2O, 25 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
2250 uM [U-15N] entity, 5 % D2O, 95 % H2O, 25 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
3200 uM [U-13C; U-15N] entity, 5 % D2O, 95 % H2O, 25 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
310 uMentity1
5 %D2O1
95 %H2O1
25 mMsodium phosphate1
100 mMsodium chloride1
250 uMentity[U-15N]2
5 %D2O2
95 %H2O2
25 mMsodium phosphate2
100 mMsodium chloride2
200 uMentity[U-13C; U-15N]3
5 %D2O3
95 %H2O3
25 mMsodium phosphate3
100 mMsodium chloride3
Sample conditionsIonic strength: 100 / pH: 5.5 / Pressure: ambient atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 36

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