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- PDB-2rot: Structure of chimeric variant of SH3 domain- SHH -

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Basic information

Entry
Database: PDB / ID: 2rot
TitleStructure of chimeric variant of SH3 domain- SHH
ComponentsSpectrin alpha chain, brain
KeywordsPROTEIN BINDING / SH3 / chimeric protein / alpha-spectrin / Actin capping / Actin-binding / Calcium / Calmodulin-binding / Cytoplasm / Cytoskeleton / Phosphoprotein / SH3 domain
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 / 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)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsSHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra ...SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra residues placed between 45th and 48th polypeptides' residues. Insertion of beta sheet includes 48-56 residues (KITVNGKTYE) between 45-48 of SH3-pwt (1SHG)
AuthorsKutyshenko, N.P. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, Y.A. / Gushchina, L.V. / Khristoforov, V.S. / Filimonov, V.V.
Citation
Journal: Biochim.Biophys.Acta / Year: 2009
Title: Solution structure and dynamics of the chimeric SH3 domains, SHH- and SHA-"Bergeracs".
Authors: Kutyshenko, V.P. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, Y.A. / Gushchina, L.V. / Khristoforov, V.S. / Filimonov, V.V. / Uversky, V.N.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Different folding transition states may result in the same native structure.
Authors: Viguera, A.R. / Serrano, L. / Wilmanns, M.
History
DepositionApr 10, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)8,1361
Polymers8,1361
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 8136.353 Da / Num. of mol.: 1 / Fragment: ALPHA-SPECTRIN SH3 Domain
Source method: isolated from a genetically manipulated source
Details: INSERTION OF BETA SHEET INCLUDING 47-56 RESIDUES (KITVNGKTYE) BETWEEN 47-48 OF SH3-PWT (1SHG).
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751
Sequence detailsINSERTION OF BETA SHEET INCLUDING 47-56 RESIDUES (KITVNGKTYE) BETWEEN 47-48 OF SH3-PWT (1SHG).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra residues placed between 45th and 48th polypeptides' residues. Insertion of beta sheet includes 48- ...Details: SHH was constructed on the basis of alpa-spectrin wild type SH3-domain, containing 10 extra residues placed between 45th and 48th polypeptides' residues. Insertion of beta sheet includes 48-56 residues (KITVNGKTYE) between 45-48 of SH3-pwt (1SHG)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D C(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
NMR detailsText: 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 NH chemical shifts

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Sample preparation

DetailsContents: 2.5mM [U-98% 13C; U-98% 15N] alpha-spectrin SHH, 90% H2O, 10% [U-99% 2H] D2O, 25mM [U-99% 2H] sodium acetate, 0.03% sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMalpha-spectrin SHH[U-98% 13C; U-98% 15N]1
90 %H2O1
10 %D2O[U-99% 2H]1
25 mMsodium acetate[U-99% 2H]1
0.03 %sodium azide1
Sample conditionsIonic strength: 20 / pH: 3.5 / Pressure: 74 3 / Temperature: 299 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
CYANA2.1Guntert, Mumenthaler, Wuthrich, Keller, Cornilescu, Delaglio, Bax, Bruker, Koradi, Billeterstructure solution
CYANA2.1Guntert, Mumenthaler, Wuthrich, Keller, Cornilescu, Delaglio, Bax, Bruker, Koradi, Billeterchemical shift assignment
CYANA2.1Guntert, Mumenthaler, Wuthrich, Keller, Cornilescu, Delaglio, Bax, Bruker, Koradi, Billeterdihedral angles calculation
CYANA2.1Guntert, Mumenthaler, Wuthrich, Keller, Cornilescu, Delaglio, Bax, Bruker, Koradi, Billeterprocessing
CYANA2.1Guntert, Mumenthaler, Wuthrich, Keller, Cornilescu, Delaglio, Bax, Bruker, Koradi, Billeterdata collection
CYANA2.1Guntert, Mumenthaler, Wuthrich, Keller, Cornilescu, Delaglio, Bax, Bruker, Koradi, Billeterrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1156 / NOE intraresidue total count: 268 / NOE long range total count: 402 / NOE medium range total count: 134 / NOE sequential total count: 352
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 / Maximum upper distance constraint violation: 0.24 Å
NMR ensemble rmsDistance rms dev: 0.0041 Å / Distance rms dev error: 0.0011 Å

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