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- PDB-1byy: SODIUM CHANNEL IIA INACTIVATION GATE -

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Basic information

Entry
Database: PDB / ID: 1byy
TitleSODIUM CHANNEL IIA INACTIVATION GATE
ComponentsPROTEIN (SODIUM CHANNEL ALPHA-SUBUNIT)
KeywordsMEMBRANE PROTEIN / SODIUM CHANNEL
Function / homology
Function and homology information


leucine zipper domain binding / membrane depolarization during action potential / axon initial segment / sodium ion binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / voltage-gated sodium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...leucine zipper domain binding / membrane depolarization during action potential / axon initial segment / sodium ion binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / voltage-gated sodium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dentate gyrus development / node of Ranvier / optic nerve development / voltage-gated sodium channel activity / sodium ion transport / axon development / neuronal action potential / sodium ion transmembrane transport / intercalated disc / T-tubule / myelination / determination of adult lifespan / cerebral cortex development / memory / presynaptic membrane / nervous system development / cellular response to hypoxia / neuron apoptotic process / calmodulin binding / axon / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site ...Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein type 2 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsRohl, C.A. / Boeckman, F.A. / Baker, C. / Scheuer, T. / Catterall, W.A. / Klevit, R.E.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure of the sodium channel inactivation gate.
Authors: Rohl, C.A. / Boeckman, F.A. / Baker, C. / Scheuer, T. / Catterall, W.A. / Klevit, R.E.
History
DepositionOct 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SODIUM CHANNEL ALPHA-SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)6,2661
Polymers6,2661
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)10 / 25NO VIOLATIONS >0.3 DEGREES OR 3 ANGSTROMS; LOWEST ENERGY
Representative

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Components

#1: Protein PROTEIN (SODIUM CHANNEL ALPHA-SUBUNIT)


Mass: 6266.271 Da / Num. of mol.: 1 / Fragment: INACTIVATION DOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL26 / References: UniProt: P04775

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED NOESY
12113C-EDITED NOESY
131HNHB
141HMQC-J
NMR detailsText: STRUCTURE DETERMINATION USING TRIPLE-RESONANCE NMR ON 13C, 15N-LABELED PROTEIN

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Sample preparation

DetailsContents: H2O/D2O
Sample conditionspH: 6.5 / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX750BrukerDMX7507502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATIONS >0.3 DEGREES OR 3 ANGSTROMS; LOWEST ENERGY
Conformers calculated total number: 25 / Conformers submitted total number: 10

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