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- PDB-2jma: R21A Spc-SH3:P41 complex -

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Basic information

Entry
Database: PDB / ID: 2jma
TitleR21A Spc-SH3:P41 complex
Components
  • P41 peptide
  • Spectrin alpha chain, brain
KeywordsSTRUCTURAL PROTEIN / SH3 domain / p41-bound
Function / homology
Function and homology information


actin filament capping / costamere / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsThe R21A mutant of the alpha-spectrin SH3 domain (R21A Spc-SH3) in complex with P41
Authorsvan Nuland, N.A.J. / Casares, S. / Ab, E. / Eshuis, H. / Lopez-Mayorga, O. / Conejero-Lara, F.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3
Authors: Casares, S. / Ab, E. / Eshuis, H. / Lopez-Mayorga, O. / van Nuland, N.A.J. / Conejero-Lara, F.
History
DepositionOct 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin alpha chain, brain
B: P41 peptide


Theoretical massNumber of molelcules
Total (without water)8,1782
Polymers8,1782
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 / 100structures with the lowest interaction energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Spectrin alpha chain, brain / Spectrin / non-erythroid alpha chain / Fodrin alpha chain / alpha spectrin


Mass: 7143.128 Da / Num. of mol.: 1 / Fragment: SH3 domain, residues 965-1025 / Mutation: R21A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Keywords: SRC-HOMOLOGY 3 DOMAIN / References: UniProt: P07751
#2: Protein/peptide P41 peptide


Mass: 1035.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The R21A mutant of the alpha-spectrin SH3 domain (R21A Spc-SH3) in complex with P41
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY

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Sample preparation

DetailsContents: 2 mM R21A Spc-SH3, 5.2 mM P41, 90 % H2O, 10 % D2O, 20 mM d5-glycine
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMR21A Spc-SH31
5.2 mMP411
90 %H2O1
10 %D2O1
20 mMd5-glycine1
Sample conditionspH: 3.5 / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnsonstructure solution
NMRViewJohnsondata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
HADDOCK1.2Dominguez, Boelens, and Bonvindata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Final refinement in explicit solvent within ARIA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest interaction energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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