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- PDB-6f7o: NMR structure of an Odin-Sam1 stapled peptide -

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Basic information

Entry
Database: PDB / ID: 6f7o
TitleNMR structure of an Odin-Sam1 stapled peptide
ComponentsAnkyrin repeat and SAM domain-containing protein 1A
KeywordsSIGNALING PROTEIN / Sam domain / stapled peptide
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 / torsion angle dynamics
AuthorsLeone, M. / Mercurio, F.A.
CitationJournal: Bioorg. Chem. / Year: 2018
Title: Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2.
Authors: Mercurio, F.A. / Pirone, L. / Di Natale, C. / Marasco, D. / Pedone, E.M. / Leone, M.
History
DepositionDec 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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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)1,6021
Polymers1,6021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area220 Å2
ΔGint-0 kcal/mol
Surface area1710 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

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


Mass: 1601.916 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Fragment 745-757 of ANKS1A protein (Uniprot entry Q92625) with R749 and L753 mutated in MK8 (=(S)-2-(4'-pentenyl) alanine )
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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 930 uM A5ST, 90% H2O/10% D2O / Details: 90% PBS pH 7.4/10% D2O / Label: PBS / Solvent system: 90% H2O/10% D2O
SampleConc.: 930 uM / Component: A5ST / Isotopic labeling: natural abundance
Sample conditionsIonic strength: NULL Not defined / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz / Details: Cold probe

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVarianprocessing
XEASYBartels et al.chemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
UCSF Chimera1.10.1Pettersen et al.geometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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