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- PDB-2kxd: The structure of SH3-F2 -

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Basic information

Entry
Database: PDB / ID: 2kxd
TitleThe structure of SH3-F2
Components11-mer peptide,Spectrin alpha chain, non-erythrocytic 1,Spectrin alpha chain, non-erythrocytic 1
KeywordsSIGNALING PROTEIN / alpha spectrin SH3 domain / Spc-S19P20s circular permutant
Function / homology
Function and homology information


costamere / actin filament capping / 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 / Src homology 3 domains / SH3 type barrels. / 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 speciessynthetic construct (others)
Gallus gallus (chicken)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, TORSION ANGLE DYNAMICS
Model detailslowest energy, model 5
AuthorsKutyshenko, V.P. / Gushchina, L.V. / Khristoforov, V.S. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, I.u.A. / Fedyukina, D.V. / Filimonov, V.V.
Citation
#1: Journal: 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. / Bruix, M.
History
DepositionApr 30, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jan 15, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 11-mer peptide,Spectrin alpha chain, non-erythrocytic 1,Spectrin alpha chain, non-erythrocytic 1


Theoretical massNumber of molelcules
Total (without water)8,0971
Polymers8,0971
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein 11-mer peptide,Spectrin alpha chain, non-erythrocytic 1,Spectrin alpha chain, non-erythrocytic 1 / Alpha-II spectrin / Fodrin alpha chain


Mass: 8097.237 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Gallus gallus (chicken)
Gene: SPTAN1, SPTA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P07751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: THE SEQUENCE, INVOLVING POLYPROLINE LIGAND MGAPPLPPYSA AND GG LINKER, WAS CONJUGATED WITH THE N-TERMINAL OF CIRCULAR PERMUTANT S19P20s (PDB ID 1TUC) INSTEAD OF THE FIRST AMINO ACIDS GP
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CC(CO)NH
1413D (H)CCH-TOCSY-ali
1513D (H)CCH-TOCSY-aro
1613D 1H-15N TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY-ali
1913D 1H-13C NOESY-aro
11013D HNCO

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Sample preparation

DetailsContents: 1.5mM [U-98% 13C; U-98% 15N] SH3-F2-1, 20mM [U-99% 2H] sodium acetate-2, 0.03 % sodium azide-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMSH3-F2-1[U-98% 13C; U-98% 15N]1
20 mMsodium acetate-2[U-99% 2H]1
0.03 %sodium azide-31
Sample conditionsIonic strength: 20 / pH: 4 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.refinement
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
XwinNMR3.5Bruker Biospinchemical shift assignment
XwinNMR3.5Bruker Biospindihedral angle prediction
XwinNMR3.5Bruker Biospinstructure solution
XwinNMR3.5Bruker Biospindata analysis
RefinementMethod: TORSION ANGLE DYNAMICS, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE WAS DETERMINED USING DIHEDRAL ANGLES PHI AND PSI PREDICTED BY PROGRAM TALOS. H-BONDS WERE DETERMINED ON THE BASIS OF TEMPERATURE DEPENDENCE OF HN CHEMICAL SHIFTS.
NMR constraintsNOE constraints total: 988 / NOE intraresidue total count: 237 / NOE long range total count: 346 / NOE medium range total count: 89 / NOE sequential total count: 316
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 5

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