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- PDB-2myq: NMR structure of an Odin-Sam1 fragment -

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Basic information

Entry
Database: PDB / ID: 2myq
TitleNMR structure of an Odin-Sam1 fragment
ComponentsAnkyrin repeat and SAM domain-containing protein 1A
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


substrate-dependent cell migration / neuron remodeling / ephrin receptor signaling pathway / ephrin receptor binding / neuron projection / nucleoplasm / 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) / SAM domain profile. / Sterile alpha motif. ...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) / 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
Similarity search - Domain/homology
Ankyrin repeat and SAM domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsfewest violations, model1
AuthorsMercurio, F.A. / Leone, M.
CitationJournal: Chembiochem / Year: 2015
Title: Peptide Fragments of Odin-Sam1: Conformational Analysis and Interaction Studies with EphA2-Sam.
Authors: Mercurio, F.A. / Di Natale, C. / Pirone, L. / Scognamiglio, P.L. / Marasco, D. / Pedone, E.M. / Saviano, M. / Leone, M.
History
DepositionJan 30, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat and SAM domain-containing protein 1A


Theoretical massNumber of molelcules
Total (without water)4,9661
Polymers4,9661
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Ankyrin repeat and SAM domain-containing protein 1A / Odin


Mass: 4965.631 Da / Num. of mol.: 1 / Fragment: SAM 1 domain residues 715-757 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92625

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 600 uM protein, TFE/H2O 70/30 v/v / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMentity_1-11
30 %H2O-21
70 %2,2,2-trifluoroethanol-d3 (TFE-d3)-3[U-99% 2H]1
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
VnmrJVariancollection
VnmrJVarianprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Structures were calculated with cyana without further refinement
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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