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- PDB-2jmc: Chimer between Spc-SH3 and P41 -

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Basic information

Entry
Database: PDB / ID: 2jmc
TitleChimer between Spc-SH3 and P41
ComponentsSpectrin alpha chain, brain and P41 peptide chimera
KeywordsSIGNALING PROTEIN / chimer / Spc-SH3 / P41
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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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)
MethodSOLUTION NMR / simulated annealing
Model detailsChimer between Spc-SH3 and decapeptide P41 starting from circular permutant S19P20s
Authorsvan Nuland, N.A.J. / Candel, A.M. / Martinez, J.C. / Conejero-Lara, F. / Bruix, M.
CitationJournal: Febs Lett. / Year: 2007
Title: The high-resolution NMR structure of a single-chain chimeric protein mimicking a SH3-peptide complex
Authors: Candel, A.M. / Conejero-Lara, F. / Martinez, J.C. / van Nuland, N.A.J. / Bruix, M.
History
DepositionNov 2, 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 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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_contact_author / pdbx_entry_details
Remark 999 SEQUENCE The author states that the chimera is based on a circular permutant of alpha-spectrin ... SEQUENCE The author states that the chimera is based on a circular permutant of alpha-spectrin SH3, named S19P20s from PDB entry 1TUC. The original N- and C-terminus of alpha-spectrin are connected and new N- and C-termini are introduced. Residues 5-47 correspond to residues 20-62 in PDB entry 1TUC. Residues 50-63 correspond to residues 4-17 in PDB entry 1TUC. S64 corresponds to residue 19 from PDB entry 1TUC. Residues 68-77 correspond to P41 peptide, see PDB entry 2JMA.

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Structure visualization

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Assembly

Deposited unit
A: Spectrin alpha chain, brain and P41 peptide chimera


Theoretical massNumber of molelcules
Total (without water)8,4631
Polymers8,4631
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 #1lowest energy

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Components

#1: Protein Spectrin alpha chain, brain and P41 peptide chimera / Spectrin / non-erythroid alpha chain / Fodrin alpha chain


Mass: 8462.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: P07751
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Chimer between Spc-SH3 and decapeptide P41 starting from circular permutant S19P20s
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1623D 1H-15N NOESY
1723D 1H-15N TOCSY
1832D 1H-1H NOESY
1922D 1H-15N HSQC
11022D 1H-15N HSQC
11113D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] SPCp41, 20 mM glycine, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM [U-98% 15N] SPCp41, 20 mM glycine, 90% H2O, 10% D2O90% H2O/10% D2O
31 mM SPCp41, 20 mM glycine, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSPCp41[U-98% 13C; U-98% 15N]1
20 mMglycine1
1 mMSPCp41[U-98% 15N]2
20 mMglycine2
1 mMSPCp413
20 mMglycine3
Sample conditionspH: 3.5 / Pressure: 1 atm / Temperature: 303.150000 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian Uniform NMR SystemVarianUniform NMR System6002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
SparkyGoddardstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnsondata analysis
NMRViewJohnsonstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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