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- PDB-2e45: Solution structure of Fe65 WW domain -

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Basic information

Entry
Database: PDB / ID: 2.0E+45
TitleSolution structure of Fe65 WW domain
ComponentsAmyloid beta A4 precursor protein-binding family B member 1
KeywordsPROTEIN BINDING / triple-stranded beta-sheet
Function / homology
Function and homology information


negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization ...negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / amyloid-beta binding / histone binding / growth cone / molecular adaptor activity / transcription coactivator activity / nuclear speck / positive regulation of apoptotic process / ubiquitin protein ligase binding / synapse / DNA damage response / chromatin binding / regulation of DNA-templated transcription / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Amyloid beta precursor protein binding family B member 1/2/3 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily ...Amyloid beta precursor protein binding family B member 1/2/3 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / 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 / PH-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Amyloid beta precursor protein binding family B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKouno, T. / Mizuguchi, M. / Nozawa, Y. / Sugaya, T. / Kawano, K.
CitationJournal: to be published
Title: Solution structure of Fe65 WW domain
Authors: Kouno, T. / Mizuguchi, M. / Nozawa, Y. / Sugaya, T. / Kawano, K.
History
DepositionDec 4, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _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: Amyloid beta A4 precursor protein-binding family B member 1


Theoretical massNumber of molelcules
Total (without water)6,1011
Polymers6,1011
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family B member 1 / Fe65 protein


Mass: 6101.491 Da / Num. of mol.: 1 / Fragment: WW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00213

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1323D 13C-separated NOESY
1422D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.65mM Fe65 WW domain U-15N, 13C; 10mM phosphate buffer NA; 90% H2O, 10% D2O90% H2O/10% D2O
20.65mM Fe65 WW domain U-15N, 13C; 10mM phosphate buffer NA; 100% D2O100% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F. Delaglio, et al.processing
PIPP4.3.2D.S. Garretcollection
X-PLOR3.1fA.T. Brungerstructure solution
X-PLOR3.1fA.T. Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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