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- PDB-8cf4: SH3 domain solved by the exact solid-state method from the Bruker... -

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Basic information

Entry
Database: PDB / ID: 8cf4
TitleSH3 domain solved by the exact solid-state method from the Bruker Dynamics Center using the combined correction method with PDB 2NUZ
ComponentsSpectrin alpha chain, non-erythrocytic 1
KeywordsPEPTIDE BINDING PROTEIN / solid-state NMR spectroscopy / structure elucidation / integrated structural biology / protein dynamics
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 domain / EF-hand domain pair ...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 domain / EF-hand domain pair / EF-hand, calcium binding motif / 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
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLID-STATE NMR / simulated annealing
AuthorsSoeldner, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)27112786 Germany
German Research Foundation (DFG)325871075 Germany
CitationJournal: J Phys Chem Lett / Year: 2023
Title: Integrated Assessment of the Structure and Dynamics of Solid Proteins.
Authors: Soldner, B. / Grohe, K. / Neidig, P. / Auch, J. / Blach, S. / Klein, A. / Vasa, S.K. / Schafer, L.V. / Linser, R.
History
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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:
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Assembly

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


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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7229.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07751

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D S2B pulse sequence with MOCCA-mixing between carbons
121isotropic25D S2B combined with a simultaneous 4D (H)CCH
131isotropic115 time-shared 15N/13C-edited H-RFDR-h(N/C)H RFDR pulse sequence with 1H-1H homonuclear mixing times from 150 us to 1.9 ms

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Sample preparation

DetailsType: solid
Contents: 1 na [U-100% 13C; U-100% 15N] SH3 of chicken alpha-spectrin, 100% H2O
Label: 1H_13C_15N_labeled_SH3 / Solvent system: 100% H2O
SampleConc.: 1 na / Component: SH3 of chicken alpha-spectrin / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 M / Label: 1H_13C_15N_labeled_SH3 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO8001CPMAS 0.7 mm H/C/N/D standard bore probe at 110 kHz MAS frequency
Bruker AVANCE NEOBrukerAVANCE NEO7002CPMAS 0.7 mm H/C/N standard bore probe at 110 kHz MAS frequency

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.5.2Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides, Ernest D. Lauechemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CcpNmr Analysis2.5.2Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides, Ernest D. Lauepeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
Details: Water refinement of the 10 lowest energy structures
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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