[English] 日本語
Yorodumi
- PDB-1jq2: POTASSIUM CHANNEL (KCSA) OPEN GATE MODEL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jq2
TitlePOTASSIUM CHANNEL (KCSA) OPEN GATE MODEL
ComponentsVOLTAGE-GATED POTASSIUM CHANNEL
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNEL / INTEGRAL MEMBRANE PROTEIN / OPEN STATE
Function / homologyVoltage-gated potassium channel / Potassium channel domain / Ion channel / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding / 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
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
Category: database_2 / pdbx_nmr_software / 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 50STRUCTURES WITH THE LOWEST PENALTY
Representative

-
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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: CONTINUOUS WAVE EPR

-
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 71 atm150.0 K
220 mM CITRATE PHOSPHATE 41 atm150.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
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 ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST PENALTY
Conformers calculated total number: 50 / Conformers submitted total number: 50

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more