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- PDB-2kd3: NMR structure of the Wnt modulator protein Sclerostin -

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Basic information

Entry
Database: PDB / ID: 2kd3
TitleNMR structure of the Wnt modulator protein Sclerostin
ComponentsSclerostin
KeywordsPROTEIN BINDING / Protein / antagonist of CYTOKINE
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 / transcription factor binding / negative regulation of BMP signaling pathway / negative regulation of protein-containing complex assembly / response to mechanical stimulus / ossification ...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 / transcription factor binding / negative regulation of BMP signaling pathway / negative regulation of protein-containing complex assembly / response to mechanical stimulus / ossification / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / heparin binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein-containing complex / extracellular space
Similarity search - Function
Sclerostin / Sclerostin/Sclerostin domain-containing protein 1 / Sclerostin (SOST) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Sclerostin / Sclerostin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWeidauer, S.E. / Mueller, T.D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: NMR structure of the Wnt modulator protein Sclerostin
Authors: Weidauer, S.E. / Schmieder, P. / Beerbaum, M. / Schmitz, W. / Oschkinat, H. / Mueller, T.D.
History
DepositionJan 2, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 10, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sclerostin


Theoretical massNumber of molelcules
Total (without water)12,7121
Polymers12,7121
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)15 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Sclerostin / Wnt modulator protein


Mass: 12711.731 Da / Num. of mol.: 1 / Fragment: mSOST deltaNC, UNP residues 59-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: B2RQA5, UniProt: Q99P68*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D CBCA(CO)NH
1233D CBCANNH
1333D HBHA(CO)NH
1433D HN(CA)CO
1533D HNCO
1633D C(CO)NH
1733D H(CCO)NH
1833D (H)CCH-TOCSY
1933D (H)CCH-COSY
11033D 1H-13C NOESY
11123D 1H-15N NOESY
11223D 1H-15N TOCSY
11323D 1H-15N HSQC-NOE-HMQC
11433D 1H-13C NOESY
11512D 1H-1H TOCSY
11612D DQF-COSY
11712D 1H-1H NOESY
11822D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Wnt modulator protein-1, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-95% 15N] Wnt modulator protein-2, 95% H2O/5% D2O95% H2O/5% D2O
30.6 mM [U-95% 13C; U-95% 15N] Wnt modulator protein-3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMWnt modulator protein-11
0.8 mMWnt modulator protein-2[U-95% 15N]2
0.6 mMWnt modulator protein-3[U-95% 13C; U-95% 15N]3
Sample conditionsIonic strength: 0.07 / pH: 6.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospinprocessing
AURELIA3.8Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerdata analysis
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1143 / NOE intraresidue total count: 471 / NOE long range total count: 317 / NOE medium range total count: 75 / NOE sequential total count: 280
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15 / Representative conformer: 1

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