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- PDB-2kiv: AIDA-1 SAM domain tandem -

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Basic information

Entry
Database: PDB / ID: 2kiv
TitleAIDA-1 SAM domain tandem
ComponentsAnkyrin repeat and sterile alpha motif domain-containing protein 1B
KeywordsSIGNALING PROTEIN / SAM domain / tandem / Alternative splicing / ANK repeat / Cell junction / Cell membrane / Cell projection / Cytoplasm / Membrane / Nucleus / Phosphoprotein / Postsynaptic cell membrane / Synapse
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 / : / Transcription Factor, Ets-1 / 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) / SAM domain profile. ...Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 1 / Ankyrin repeat and SAM domain-containing protein 1, SAM repeat 2 / : / Transcription Factor, Ets-1 / 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) / 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 / DNA polymerase; domain 1 / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
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.W. / Kurabi, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: A nuclear localization signal at the SAM-SAM domain interface of AIDA-1 suggests a requirement for domain uncoupling prior to nuclear import.
Authors: Kurabi, A. / Brener, S. / Mobli, M. / Kwan, J.J. / Donaldson, L.W.
History
DepositionMay 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 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)16,6721
Polymers16,6721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the least restraint violations
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: 16672.158 Da / Num. of mol.: 1 / Fragment: SAM1 and SAM2 domains / Mutation: F30A, Y73A, W109A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIDA-1b, ANKS1B / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21:DE3 / 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
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D C(CO)NH
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D HNCO
11113D H(CCO)NH

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Sample preparation

DetailsContents: 1.1 mM [U-99% 13C; U-99% 15N] protein, 10 % D2O, 90 % H2O, 0.05 % sodium azide, 5 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMentity[U-99% 13C; U-99% 15N]1
10 %D2O1
90 %H2O1
0.05 %sodium azide1
5 mMsodium phosphate1
50 mMsodium chloride1
Sample conditionsIonic strength: 0.05 / pH: 7.8 / Pressure: ambient / Temperature: 298 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 softwareName: CYANA / Version: 2.1 / Developer: Guntert, P. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 15000 steps of SA using the standard CYANA calc_all protocol
NMR constraintsNOE constraints total: 2008 / NOE intraresidue total count: 864 / NOE long range total count: 413 / NOE medium range total count: 264 / NOE sequential total count: 343
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.13 Å
NMR ensemble rmsDistance rms dev: 0.0072 Å / Distance rms dev error: 0.0013 Å

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