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- PDB-2ke7: NMR structure of the first SAM domain from AIDA1 -

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Basic information

Entry
Database: PDB / ID: 2ke7
TitleNMR structure of the first SAM domain from AIDA1
ComponentsAnkyrin repeat and sterile alpha motif domain-containing protein 1B
KeywordsPROTEIN BINDING / SAM domain / 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 / torsion angle dynamics, simulated annealing
AuthorsDonaldson, L.
CitationJournal: To be Published
Title: NMR structure of the first SAM domain from AIDA1
Authors: Donaldson, L.
History
DepositionJan 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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

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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)11,5021
Polymers11,5021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ankyrin repeat and sterile alpha motif domain-containing protein 1B


Mass: 11502.014 Da / Num. of mol.: 1 / Fragment: first SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: This vector is from the NIH structural genomics consortium. It contains a His6 tag, Maltose Binding Protein tag and a TEV protease cleavage site
Gene: ANKS1B / Plasmid: pDEST586 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / 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 CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
NMR detailsText: This structure was determined using NOE restraints and dihedral angle restraints predicted from chemical shifts

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Sample preparation

DetailsContents: 0.8 mM [U-98% 13C; U-98% 15N] AIDA1 SAM1-1, 10 % D2O-2, 90 % H2O-3, 150 mM sodium chloride-4, 20 mM sodium phosphate-5, 0.05 % sodium azide-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMAIDA1 SAM1-1[U-98% 13C; U-98% 15N]1
10 %D2O-21
90 %H2O-31
150 mMsodium chloride-41
20 mMsodium phosphate-51
0.05 %sodium azide-61
Sample conditionsIonic strength: 0.15 / pH: 7.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian NMRS / Manufacturer: Varian / Model: NMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.21Schwieters, C.D. et al.refinement
NMRView5Johnson, B. et al.peak picking
CYANA2.1Guntert, P. et al.structure solution
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: 5000 steps using CYANA standard torsion angle dynamics, water-refinement using XPLOR-NIH and cartesian dynamics. Specifics: 2000 hot steps at 500 K, 500 cool steps to 100 K final in 100 K increments
NMR constraintsNOE constraints total: 661 / NOE intraresidue total count: 351 / NOE long range total count: 86 / NOE medium range total count: 66 / NOE sequential total count: 158
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.5 Å / Maximum upper distance constraint violation: 0.5 Å

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