[English] 日本語
Yorodumi
- PDB-1qdv: N-TERMINAL DOMAIN, VOLTAGE-GATED POTASSIUM CHANNEL KV1.2 RESIDUES... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qdv
TitleN-TERMINAL DOMAIN, VOLTAGE-GATED POTASSIUM CHANNEL KV1.2 RESIDUES 33-131
ComponentsKV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
KeywordsSIGNALING PROTEIN / VOLTAGE-GATED POTASSIUM CHANNEL / TETRAMERIZATION DOMAIN / INTRACELLULAR GATE / TETRAMER
Function / homology
Function and homology information


optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / axon initial segment / delayed rectifier potassium channel activity / corpus callosum development ...optic nerve structural organization / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / axon initial segment / delayed rectifier potassium channel activity / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / outward rectifier potassium channel activity / juxtaparanode region of axon / optic nerve development / neuronal cell body membrane / regulation of dopamine secretion / voltage-gated potassium channel activity / lamellipodium membrane / kinesin binding / neuronal action potential / calyx of Held / voltage-gated potassium channel complex / axon terminus / sensory perception of pain / potassium ion transmembrane transport / protein homooligomerization / cerebral cortex development / presynaptic membrane / lamellipodium / perikaryon / postsynaptic membrane / endosome / axon / dendrite / glutamatergic synapse / endoplasmic reticulum 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 / 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 ...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 / 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. / Yu, M. / 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
DepositionJul 10, 1999Deposition 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 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
B: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
C: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL
D: KV1.2 VOLTAGE-GATED POTASSIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)47,8144
Polymers47,8144
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.768, 86.026, 96.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 11953.511 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 33-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / References: UniProt: P63142
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19% PEG 4000, 100 MM NH4 ACETATE, 21% METHANOL, MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
219 %PEG40001reservoir
3100 mM1reservoirNH4C2H3O2
421 %methanol1reservoir
550 mMMES1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 57516 / Num. obs: 49725 / % possible obs: 86.4 % / Redundancy: 6.78 % / Biso Wilson estimate: 22.379 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.166 / % possible all: 67.6
Reflection
*PLUS
Rmerge(I) obs: 0.03

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→20 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.278 4972 RANDOM
Rwork0.238 --
all-57516 -
obs-49725 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 236 3608
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / Rfactor obs: 0.238 / % reflection Rfree: 10 %
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