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- PDB-1jq1: POTASSIUM CHANNEL (KCSA) OPEN GATE MODEL -

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Basic information

Entry
Database: PDB / ID: 1jq1
TitlePOTASSIUM CHANNEL (KCSA) OPEN GATE MODEL
ComponentsVOLTAGE-GATED POTASSIUM CHANNEL
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNEL / INTEGRAL MEMBRANE PROTEIN / OPEN STATE
Function / homologyPotassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / pH-gated potassium channel KcsA
Function and homology information
Biological speciesStreptomyces lividans (bacteria)
MethodSOLUTION NMR / FOURIER DECONVOLUTION, CONFORMATIONAL GRID SEARCH A CARTESAIN REPRESENTATION MOLECULAR MECHANIC ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsLiu, Y.-S. / Sompornpisut, P. / Perozo, E.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the KcsA channel intracellular gate in the open state.
Authors: Liu, Y.S. / Sompornpisut, P. / Perozo, E.
#1: Journal: TO BE PUBLISHED
Title: Calculation of Rigid Body Conformational Changes Using Restraint-Driven Cartesian Transformations
Authors: Sompornpisut, P. / Liu, Y.-S. / Perozo, E.
#2: Journal: Science / Year: 1999
Title: Structural Rearrangements Underlying K+-Channel Activation Gating
Authors: Perozo, E. / Cortes, D.M. / Cuello, L.G.
#3: Journal: Science / Year: 1998
Title: The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity
Authors: Doyle, D.A. / Morais Cabral, J. / Pfuetzner, R.A. / Kuo, A. / Gulbis, J.M. / Cohen, S.L. / Chait, B.T. / Mackinnon, R.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Remark 99The structure contains only alpha-carbons because the experimental data used to calculate the ...The structure contains only alpha-carbons because the experimental data used to calculate the structures are good enough only to the backbone level.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VOLTAGE-GATED POTASSIUM CHANNEL
B: VOLTAGE-GATED POTASSIUM CHANNEL
C: VOLTAGE-GATED POTASSIUM CHANNEL
D: VOLTAGE-GATED POTASSIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)14,4454
Polymers14,4454
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein/peptide
VOLTAGE-GATED POTASSIUM CHANNEL / / Coordinate model: Cα atoms only


Mass: 3611.283 Da / Num. of mol.: 4 / Fragment: INNER TRANSMEMBRANE SEGMENT (residues 86-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Plasmid: PQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-2 BLUE / References: UniProt: P0A334

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: CONTINUOUS WAVE EPR

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Sample preparation

DetailsContents: 1.0 MG/ML MIXED WITH METHANETHIOSULFONATE SPIN LABEL
Solvent system: THE SAMPLES WERE RECONSTITUTED INTO ASOLECTIN LIPOSOMES AT A 1:400 PROTEIN:LIPID RATIO
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM CITRATE PHOSPHATE 7.0 1 atm150.0 K
220 mM CITRATE PHOSPHATE 4.0 1 atm150.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker EMX / Manufacturer: Bruker / Model: EMX / Field strength: 3400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber6D.A.CASE ET.AL.refinement
EPR AQUISIT2.32BRUKERprocessing
REDCATP.SOMPORNPISUT ET.AL.structure solution
RefinementMethod: FOURIER DECONVOLUTION, CONFORMATIONAL GRID SEARCH A CARTESAIN REPRESENTATION MOLECULAR MECHANIC ENERGY MINIMIZATION
Software ordinal: 1
Details: THE STRUCTURE ARE BASED ON: 1) TEN PAIRS OF INTER-SUBUNIT DISTANCES FOR THE KCSA INNER HELICAL BUNDLE IN THE CLOSED AND THE OPEN STATES AND 2) THE USE OF THE CRYSTAL STRUCTURE AS THE CHANNEL ...Details: THE STRUCTURE ARE BASED ON: 1) TEN PAIRS OF INTER-SUBUNIT DISTANCES FOR THE KCSA INNER HELICAL BUNDLE IN THE CLOSED AND THE OPEN STATES AND 2) THE USE OF THE CRYSTAL STRUCTURE AS THE CHANNEL IN THE CLOSED STATE, AND AS THE REFERENCE STRUCTURE. THE COMPUTER PROGRAM REDCAT SEARCHES (RESTRAINT-DRIVEN CARTESIAN TRANSFORMATION) BASED ON THE EXHAUSTIVE SAMPLING OF RIGID-BODY MOVEMENT IN CARTESIAN SPACE FOR THE TM2 INNER BUNDLE IN THE OPEN STATE WERE ALLOWED TO CONVERGE TO A MINIMAL PENALTY VALUE. THE ENSEMBLE OF THE 50 LOWEST PENALTY CONFORMERS WAS SUBJECTED TO MOLECULAR MECHANIC ENERGY MINIMIZATION. FINAL REFINEMENT WAS PERFORMED ON THE AVERAGE OPEN HELICAL BUNDLE BY ENERGY MINIMIZATION.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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