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- PDB-2e6w: Solution structure and calcium binding properties of EF-hands 3 a... -

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Basic information

Entry
Database: PDB / ID: 2e6w
TitleSolution structure and calcium binding properties of EF-hands 3 and 4 of calsenilin
ComponentsCalsenilin
KeywordsMETAL BINDING PROTEIN / Calcium-bound form
Function / homology
Function and homology information


Phase 1 - inactivation of fast Na+ channels / voltage-gated monoatomic ion channel activity / regulation of potassium ion transmembrane transport / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / axon terminus / protein localization to plasma membrane / protein-DNA complex / intracellular protein transport ...Phase 1 - inactivation of fast Na+ channels / voltage-gated monoatomic ion channel activity / regulation of potassium ion transmembrane transport / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / axon terminus / protein localization to plasma membrane / protein-DNA complex / intracellular protein transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / transmembrane transporter binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / apoptotic process / calcium ion binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / nucleus / plasma membrane / cytosol
Similarity search - Function
Recoverin family / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...Recoverin family / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsYu, L. / Sun, C. / Mendoza, R. / Hebert, E. / Pereda-Lopez, A. / Hajduk, P.J. / Olejniczak, E.T.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure and calcium-binding properties of EF-hands 3 and 4 of calsenilin.
Authors: Yu, L. / Sun, C. / Mendoza, R. / Wang, J. / Matayoshi, E.D. / Hebert, E. / Pereda-Lopez, A. / Hajduk, P.J. / Olejniczak, E.T.
History
DepositionJan 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calsenilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8893
Polymers11,8081
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein Calsenilin / DRE-antagonist modulator / DREAM / Kv channel-interacting protein 3 / KChIP3 / A-type potassium ...DRE-antagonist modulator / DREAM / Kv channel-interacting protein 3 / KChIP3 / A-type potassium channel modulatory protein 3


Mass: 11808.465 Da / Num. of mol.: 1 / Fragment: EF-hands 3 and 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DREAM, KCHIP3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2W7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM Calsenilin, 25mM Tris-HCl, 5mM DTT, 15mM CaCl2; 90% H2O, 10% D2O90% H2O/10% D2O
21.0mM Calsenilin, 25mM Tris-HCl, 5mM DTT, 15mM CaCl2; 100% D2O100% D2O
Sample conditionspH: 8.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNX2000A.T.Brunger at al.structure solution
CNX2000A.T.Brunger at al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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