[English] 日本語
Yorodumi
- PDB-1dsx: KV1.2 T1 DOMAIN, RESIDUES 33-119, T46V MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dsx
TitleKV1.2 T1 DOMAIN, RESIDUES 33-119, T46V MUTANT
ComponentsPROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
KeywordsSIGNALING PROTEIN / VOLTAGE-GATED POTASSIUM CHANNEL / ASSEMBLY DOMAIN / TETRAMER
Function / homology
Function and homology information


optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity ...optic nerve structural organization / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / axon initial segment / optic nerve development / juxtaparanode region of axon / outward rectifier potassium channel activity / neuronal cell body membrane / regulation of dopamine secretion / lamellipodium membrane / action potential / kinesin binding / voltage-gated potassium channel activity / neuronal action potential / axon terminus / voltage-gated potassium channel complex / potassium ion transmembrane transport / sensory perception of pain / calyx of Held / protein homooligomerization / cerebral cortex development / lamellipodium / presynaptic membrane / perikaryon / postsynaptic membrane / endosome / axon / dendrite / endoplasmic reticulum membrane / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain ...Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMinor Jr., D.L. / Lin, Y.-F. / Mobley, B.C. / Avelar, A. / Jan, Y.N. / Jan, L.Y. / Berger, J.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: The polar T1 interface is linked to conformational changes that open the voltage-gated potassium channel.
Authors: Minor, D.L. / Lin, Y.F. / Mobley, B.C. / Avelar, A. / Jan, Y.N. / Jan, L.Y. / Berger, J.M.
History
DepositionJan 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
B: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
C: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
D: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
E: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
F: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
G: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
H: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Theoretical massNumber of molelcules
Total (without water)83,9688
Polymers83,9688
Non-polymers00
Water9,926551
1
A: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
B: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
C: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
D: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Theoretical massNumber of molelcules
Total (without water)41,9844
Polymers41,9844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
F: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
G: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)
H: PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Theoretical massNumber of molelcules
Total (without water)41,9844
Polymers41,9844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.390, 78.398, 126.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
PROTEIN (KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL)


Mass: 10495.991 Da / Num. of mol.: 8 / Fragment: N-TERMINAL ASSEMBLY DOMAIN, RESIDUES 33-119 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PET24 / Production host: Escherichia coli (E. coli) / References: UniProt: P63142
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growpH: 8.5
Details: 22% PEG 1500, 5 % ISOPROPANOL, 200 MM NA ACETATE, 12 MM SRCL2, 50 MM TRIS, PH 8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
222 %PEG15001reservoir
35 %isopropanol1reservoir
4200 mM1reservoirNaC2H3O2
512 mM1reservoirSrCl2
650 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Aug 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 97159 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.75 Å / Rmerge(I) obs: 0.371 / % possible all: 84.4
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 23.1 Å2

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.279 9715 RANDOM
Rwork0.237 --
obs-97159 -
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5944 0 0 555 6499
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

+
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