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- PDB-2m38: PTB domain of AIDA1 -

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Basic information

Entry
Database: PDB / ID: 2m38
TitlePTB domain of AIDA1
ComponentsAnkyrin repeat and sterile alpha motif domain-containing protein 1B
KeywordsPEPTIDE BINDING PROTEIN / PHOSPHOTYROSINE BINDING DOMAIN
Function / homology
Function and homology information


ephrin receptor signaling pathway / Cajal body / ephrin receptor binding / dendritic spine / postsynaptic density / centrosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SAM domain (Sterile alpha motif) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SAM domain (Sterile alpha motif) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Ankyrin repeat and sterile alpha motif domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDonaldson, L.
CitationJournal: Plos One / Year: 2013
Title: Solution structure and peptide binding of the PTB domain from the AIDA1 postsynaptic signaling scaffolding protein.
Authors: Smirnova, E. / Shanbhag, R. / Kurabi, A. / Mobli, M. / Kwan, J.J. / Donaldson, L.W.
History
DepositionJan 14, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat and sterile alpha motif domain-containing protein 1B


Theoretical massNumber of molelcules
Total (without water)17,0661
Polymers17,0661
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 / 20all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein Ankyrin repeat and sterile alpha motif domain-containing protein 1B / Amyloid-beta protein intracellular domain-associated protein 1 / AIDA-1 / E2A-PBX1-associated protein / EB-1


Mass: 17065.555 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE BINDING DOMAIN / Mutation: Y6A, F16A, F24A, Y70A, Y131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKS1B / Plasmid: pJExpress405 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6G8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC NH2 only
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.8 mM PTB domain, 20 mM sodium phosphate, 150 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.8 mMPTB domain1
20 mMsodium phosphate-11
150 mMsodium chloride-21
0.05 %sodium azide-31
Sample conditionsIonic strength: 0.15 / pH: 7.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: initial ensemble of 200 structures choosing best 20 with CYANA, water refinement of 20 structures with XPLOR-NIH
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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