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- PDB-2kr3: Solution structure of SHA-D -

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Basic information

Entry
Database: PDB / ID: 2kr3
TitleSolution structure of SHA-D
ComponentsSpectrin alpha chain, brain
KeywordsSIGNALING PROTEIN / alpha spectrin SH3 domain / Bergerac / Actin capping / Actin-binding / Cytoskeleton
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 / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKhristoforov, V.S. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, Y.A. / Gushchina, L.V. / Filimonov, V.V. / Kutyshenko, V.P.
Citation
Journal: Russ.J.Bioorganic Chem. / Year: 2010
Title: Chimeric SHA-D domain "SH3-Bergerac": 3D structure and dynamics studies
Authors: Khristoforov, V.S. / Prokhorov, D.A. / Timchenko, M.A. / Kudrevatykh, Y.A. / Gushchina, L.V. / Filimonov, V.V. / Kutyshenko, V.P.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus
Authors: Viguera, A.-R. / Serrano, L.
History
DepositionDec 3, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)8,1241
Polymers8,1241
Non-polymers00
Water0
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 Spectrin alpha chain, brain / sha-d / Spectrin / non-erythroid alpha chain / Fodrin alpha chain


Mass: 8124.256 Da / Num. of mol.: 1 / Fragment: alpha spectrin SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: sha-d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P07751
Sequence detailsTHIS IS ANALOGUE OF SHA PROTEIN. THERE IS INSERTION OF BETA SHEET INCLUDING 47-56 RESIDUES ...THIS IS ANALOGUE OF SHA PROTEIN. THERE IS INSERTION OF BETA SHEET INCLUDING 47-56 RESIDUES (KATANDKTYE) BETWEEN 46-49 OF SH3-PWT (1SHG).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
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] SHA-D; 20mM [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
1.5 mMSHA-D-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: 3.5 / 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
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
XwinNMR3.5Bruker Biospincollection
CARAKeller and Wuthrichprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxchemical shift calculation
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 851 / NOE intraresidue total count: 200 / NOE long range total count: 288 / NOE medium range total count: 79 / NOE sequential total count: 284
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: 1

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