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- PDB-6scw: SH3-subunit of chicken alpha spectrin solved by NMR -

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Basic information

Entry
Database: PDB / ID: 6scw
TitleSH3-subunit of chicken alpha spectrin solved by NMR
ComponentsSpectrin alpha chain, non-erythrocytic 1 isoform X11
KeywordsPEPTIDE BINDING PROTEIN / beta-barrel / binding-domain / membrane-ancor / spectrin
Function / homology
Function and homology information


cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / plasma membrane
Similarity search - Function
Alpha Spectrin, SH3 domain / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1 isoform X11 / :
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / simulated annealing
AuthorsGrohe, K. / Hebrank, C. / Linser, R.
CitationJournal: Structure / Year: 2020
Title: Protein Motional Details Revealed by Complementary Structural Biology Techniques.
Authors: Grohe, K. / Patel, S. / Hebrank, C. / Medina, S. / Klein, A. / Rovo, P. / Vasa, S.K. / Singh, H. / Vogeli, B. / Schafer, L.V. / Linser, R.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 31, 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: Spectrin alpha chain, non-erythrocytic 1 isoform X11


Theoretical massNumber of molelcules
Total (without water)7,2291
Polymers7,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 800target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Spectrin alpha chain, non-erythrocytic 1 isoform X11


Mass: 7229.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A480YJK9, UniProt: A0A480YEE4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic13D HNHA
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 12 mg/L 15N, 13C SH3-domain of chicken alpha spectrin, 95% H2O/5% D2O
Details: solution state NMR-sample in citric acid buffer at pH 3.5 and 298 K
Label: 15N, 13C / Solvent system: 95% H2O/5% D2O
SampleConc.: 12 mg/L / Component: SH3-domain of chicken alpha spectrin / Isotopic labeling: 15N, 13C
Sample conditionsIonic strength: 3 (cirtic acid) M / Label: 13C, 15N / pH: 3.5 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.7Bruker Biospinprocessing
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.1CCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: 200000 steps
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 800 / Conformers submitted total number: 10

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