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- PDB-5o57: Solution Structure of the N-terminal Region of Dkk4 -

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Basic information

Entry
Database: PDB / ID: 5o57
TitleSolution Structure of the N-terminal Region of Dkk4
ComponentsDickkopf-related protein 4
KeywordsSIGNALING PROTEIN / Dkk4 / Wnt Signalling / Cysteine-rich domain 1
Function / homology
Function and homology information


negative regulation of hair follicle placode formation / Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / receptor antagonist activity / co-receptor binding / multicellular organism development / negative regulation of Wnt signaling pathway / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / extracellular space
Similarity search - Function
Prokineticin domain / Prokineticin / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / Dickkopf N-terminal cysteine-rich region
Similarity search - Domain/homology
Dickkopf-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWaters, L.C. / Patel, S. / Barkell, A.M. / Muskett, F.W. / Robinson, M.K. / Holdsworth, G. / Carr, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional analysis of Dickkopf 4 (Dkk4): New insights into Dkk evolution and regulation of Wnt signaling by Dkk and Kremen proteins.
Authors: Patel, S. / Barkell, A.M. / Gupta, D. / Strong, S.L. / Bruton, S. / Muskett, F.W. / Addis, P.W. / Renshaw, P.S. / Slocombe, P.M. / Doyle, C. / Clargo, A. / Taylor, R.J. / Prosser, C.E. / ...Authors: Patel, S. / Barkell, A.M. / Gupta, D. / Strong, S.L. / Bruton, S. / Muskett, F.W. / Addis, P.W. / Renshaw, P.S. / Slocombe, P.M. / Doyle, C. / Clargo, A. / Taylor, R.J. / Prosser, C.E. / Henry, A.J. / Robinson, M.K. / Waters, L.C. / Holdsworth, G. / Carr, M.D.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 2.0Jul 4, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.1Aug 15, 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
Revision 2.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.3Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 2.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dickkopf-related protein 4


Theoretical massNumber of molelcules
Total (without water)10,9311
Polymers10,9311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10250 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)70 / 100target function
RepresentativeModel #13closest to the average

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Components

#1: Protein Dickkopf-related protein 4 / hDkk-4


Mass: 10931.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKK4 / Plasmid: pLEICS-05 / Details (production host): University of Leicester vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9UBT3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D TROSY-HN(CA)CB
121isotropic13D TROSY-HN(CO)CACB
131isotropic13D TROSY-HNCO
141isotropic13D HBHA(CO)NH
151isotropic12D TROSY
163isotropic12D 1H-1H TOCSY
173isotropic12D 1H-1H NOESY
184isotropic13D (H)CCH-TOCSY
195isotropic33D 13C/1H HSQC-NOESY
1105isotropic23D 13C/1H HSQC-NOESY
1112isotropic23D 15N/1H NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1140 uM [U-13C; U-15N] Dkk4n, 95% H2O/5% D2ODkk4n15N_13C_Dkk4n95% H2O/5% D2ODkk4n
solution2210 uM [U-15N] Dkk4n, 95% H2O/5% D2O15N_Dkk4n95% H2O/5% D2O
solution390 uM [U-15N] Dkk4n, 100% D2O15N_Dkk4n_(D2O)100% D2O
solution4140 uM [U-13C; U-15N] Dkk4n, 100% D2O15N_13C_Dkk4n_(D2O)100% D2O
solution5230 uM [U-13C; U-15N] Dkk4n, 100% D2O15N_13C_Dkkn_(D2O)_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
140 uMDkk4n[U-13C; U-15N]1
210 uMDkk4n[U-15N]2
90 uMDkk4n[U-15N]3
140 uMDkk4n[U-13C; U-15N]4
230 uMDkk4n[U-13C; U-15N]5
Sample conditionsDetails: 25mM Sodium Phosphate, 100mM Sodium Chloride, 0.02% (w/v) Sodium Azide, pH 6.5
Ionic strength: 150 mM / Label: Conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVIIIBrukerAVIII6001
Bruker AVIIBrukerAVII8002
Bruker AVANCE III HDBrukerAVANCE III HD9503

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyNMRFAM-Sparky 1.4Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: REDAC
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 70

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