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- PDB-2d46: Solution Structure of the Human Beta4a-A Domain -

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Entry
Database: PDB / ID: 2d46
TitleSolution Structure of the Human Beta4a-A Domain
Componentscalcium channel, voltage-dependent, beta 4 subunit isoform a
KeywordsMETAL TRANSPORT / Ca2+ channel / beta4a subunit / alternative spliving / membrane-associated guanylate-kinase / protein structure
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / regulation of voltage-gated calcium channel activity / positive regulation of protein localization to nucleolus / Presynaptic depolarization and calcium channel opening / gamma-aminobutyric acid secretion / detection of light stimulus involved in visual perception / cAMP metabolic process / Peyer's patch development / NCAM1 interactions / muscle cell development ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / regulation of voltage-gated calcium channel activity / positive regulation of protein localization to nucleolus / Presynaptic depolarization and calcium channel opening / gamma-aminobutyric acid secretion / detection of light stimulus involved in visual perception / cAMP metabolic process / Peyer's patch development / NCAM1 interactions / muscle cell development / neuronal action potential propagation / adult walking behavior / voltage-gated calcium channel complex / gamma-aminobutyric acid signaling pathway / neuromuscular junction development / regulation of synaptic vesicle exocytosis / negative regulation of G1/S transition of mitotic cell cycle / spleen development / cellular response to leukemia inhibitory factor / thymus development / synaptic transmission, glutamatergic / cytoplasmic side of plasma membrane / calcium ion transport / presynapse / T cell receptor signaling pathway / chemical synaptic transmission / nuclear speck / negative regulation of cell population proliferation / synapse / protein kinase binding / glutamatergic synapse / plasma membrane / cytosol
Similarity search - Function
Ybab; Chain: A; - #30 / Ybab; Chain: A; / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Ybab; Chain: A; - #30 / Ybab; Chain: A; / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit beta-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVendel, A.C. / Rithner, C.D. / Lyons, B.A. / Horne, W.A.
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of the N-terminal A domain of the human voltage-gated Ca2+channel beta4a subunit
Authors: Vendel, A.C. / Rithner, C.D. / Lyons, B.A. / Horne, W.A.
History
DepositionOct 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: calcium channel, voltage-dependent, beta 4 subunit isoform a


Theoretical massNumber of molelcules
Total (without water)6,8771
Polymers6,8771
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)1 / 15structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein calcium channel, voltage-dependent, beta 4 subunit isoform a / calcium channel beta4a subunit


Mass: 6877.298 Da / Num. of mol.: 1 / Fragment: N-terminal A domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: human cerebellum, presynaptic / Gene: CACNB4 / Plasmid: pET-15b:b4a-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O00305

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
1412D TOCSY
1512D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopic techniques.

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Sample preparation

DetailsContents: 3mM beta4a A domain, uniformly 15N and 13C labeled; 50mM sodium phosphate, 150mM NaCl, 0.1mM NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe4.1Delaglio, F.processing
NMRView5.0.4Johnson, B.data analysis
ANSIGAnsig for WindowsHelgstranddata analysis
CNS1.1Brunger, T.structure solution
CNS1.1Brunger, T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: A total of 1213 structural restraints were used to calculate determine the final 15 representative solution structures of the beta4a A domain. 963 NOE derived distance constraints were ...Details: A total of 1213 structural restraints were used to calculate determine the final 15 representative solution structures of the beta4a A domain. 963 NOE derived distance constraints were utilized in the calculation, of which 472 were intra-residue, 196 sequential, 87 medium-range (4<|i-j|>1) and 208 long-range (|i-j|≥4), providing for an average total of 15.8 NOE constraints/residue.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 15 / Conformers submitted total number: 1

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