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- PDB-1wmv: Solution structure of the second WW domain of WWOX -

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Basic information

Entry
Database: PDB / ID: 1wmv
TitleSolution structure of the second WW domain of WWOX
ComponentsWW domain containing oxidoreductase
KeywordsOXIDOREDUCTASE / APOPTOSIS / WW domain / all-beta
Function / homology
Function and homology information


Negative regulation of activity of TFAP2 (AP-2) family transcription factors / Activation of the TFAP2 (AP-2) family of transcription factors / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / positive regulation of extrinsic apoptotic signaling pathway / skeletal system morphogenesis / negative regulation of Wnt signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / Nuclear signaling by ERBB4 / cellular response to transforming growth factor beta stimulus ...Negative regulation of activity of TFAP2 (AP-2) family transcription factors / Activation of the TFAP2 (AP-2) family of transcription factors / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / positive regulation of extrinsic apoptotic signaling pathway / skeletal system morphogenesis / negative regulation of Wnt signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / Nuclear signaling by ERBB4 / cellular response to transforming growth factor beta stimulus / extrinsic apoptotic signaling pathway / Wnt signaling pathway / osteoblast differentiation / RNA polymerase II transcription regulator complex / transcription coactivator activity / lysosome / oxidoreductase activity / Golgi apparatus / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WWOX, classical (c)-like SDR domain / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / short chain dehydrogenase / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain ...WWOX, classical (c)-like SDR domain / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / short chain dehydrogenase / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
WW domain-containing oxidoreductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKowalski, K. / Merkel, A.L. / Colella, A. / Richards, R.I. / Booker, G.W.
CitationJournal: To be Published
Title: Solution structure of the second WW domain of WWOX
Authors: Kowalski, K. / Merkel, A.L. / Colella, A. / Richards, R.I. / Booker, G.W.
History
DepositionJul 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _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: WW domain containing oxidoreductase


Theoretical massNumber of molelcules
Total (without water)6,2041
Polymers6,2041
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein WW domain containing oxidoreductase / WWOX


Mass: 6203.820 Da / Num. of mol.: 1 / Fragment: second WW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WOX/FOR / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NZC7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1322D NOESY
143HNHA
NMR detailsText: This structure was calculated using NOE data derived from 1H NOESY in H2O and D2O, and dihedral angle data derived from 15N HNHA and HNHB experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75mM WW2; 25mM phosphate buffer; 100mM NaCl; 0.01% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
20.75mM WW2; 25mM phosphate buffer; 100mM NaCl; 0.01% NaN3; 100% D2O100% D2O
30.7mM WW2 U-15N; 25mM phosphate buffer; 100mM NaCl; 0.01% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglio, et alprocessing
Sparky3.11Goddard and Knellerdata analysis
CNS1.1Brunger, et alstructure solution
ARIA1.2Linge, et alstructure solution
ARIA1.2Linge, et alrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Structures are based on a total of 709 restraints; 670 NOE-derived distance rconstraints, 39 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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