[English] 日本語
Yorodumi
- PDB-6ale: A V-to-F substitution in SK2 channels causes Ca2+ hypersensitivit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ale
TitleA V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves locomotion in a C. elegans ALS model
Components
  • Calmodulin-2
  • Small conductance calcium-activated potassium channel protein 2
KeywordsMETAL TRANSPORT / Calcium binding protein
Function / homology
Function and homology information


small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / Ca2+ activated K+ channels / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / presynaptic endocytosis / establishment of protein localization to mitochondrial membrane / inward rectifier potassium channel activity / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport ...small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / Ca2+ activated K+ channels / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / presynaptic endocytosis / establishment of protein localization to mitochondrial membrane / inward rectifier potassium channel activity / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport / presynaptic cytosol / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / response to corticosterone / autophagosome membrane docking / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / protein phosphatase activator activity / adenylate cyclase binding / calyx of Held / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / calcium channel complex / potassium ion transmembrane transport / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / response to amphetamine / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / potassium ion transport / Schaffer collateral - CA1 synapse / cellular response to type II interferon / Z disc / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / vesicle / transmembrane transporter binding / dendritic spine / calmodulin binding / protein domain specific binding / centrosome / neuronal cell body / calcium ion binding / protein kinase binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / plasma membrane / cytoplasm
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1KP / Calmodulin-2 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNam, Y.W. / Zhang, M.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association13SDG16150007 United States
National Ataxia FoundationYI-SCA United States
CitationJournal: Sci Rep / Year: 2018
Title: A V-to-F substitution in SK2 channels causes Ca2+hypersensitivity and improves locomotion in a C. elegans ALS model.
Authors: Nam, Y.W. / Baskoylu, S.N. / Gazgalis, D. / Orfali, R. / Cui, M. / Hart, A.C. / Zhang, M.
History
DepositionAug 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 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
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,53910
Polymers27,7512
Non-polymers7888
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.653, 66.913, 64.712
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11R-1136-

HOH

-
Components

-
Protein , 2 types, 2 molecules BR

#1: Protein Small conductance calcium-activated potassium channel protein 2 / SKCa2 / KCa2.2


Mass: 11331.361 Da / Num. of mol.: 1 / Fragment: calmodulin binding domain (UNP residues 394-486)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2S1
#2: Protein Calmodulin-2


Mass: 16420.031 Da / Num. of mol.: 1 / Fragment: UNP residues 5-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm2, Cam2, Camb, CaMII / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP30

-
Non-polymers , 5 types, 124 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1KP / (3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one


Mass: 231.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4Cl2N2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium Citrate Tribasic dehydrate 0.6 M Ammonium sulfate 1.4 M Lithium sulfate monohydrate
PH range: 5.6-5.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: CMOS / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.72 Å / Num. obs: 11420 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 29.76 Å2 / Net I/σ(I): 13.3

-
Processing

Software
NameVersionClassification
XPREPdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHASESphasing
RefinementResolution: 2.5→24.193 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.4
RfactorNum. reflection% reflection
Rfree0.2551 548 4.8 %
Rwork0.188 --
obs0.1912 11410 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.69 Å2 / Biso mean: 45.481 Å2 / Biso min: 16.1 Å2
Refinement stepCycle: final / Resolution: 2.5→24.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 42 116 2096
Biso mean--100.74 40.2 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071996
X-RAY DIFFRACTIONf_angle_d1.1272676
X-RAY DIFFRACTIONf_chiral_restr0.051293
X-RAY DIFFRACTIONf_plane_restr0.004346
X-RAY DIFFRACTIONf_dihedral_angle_d21.1531218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.75130.33081400.237826762816
2.7513-3.14870.30231470.219927012848
3.1487-3.96420.27641310.180127202851
3.9642-24.19440.18841300.16327652895
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.53962.813-4.83092.3239-1.39633.4133-0.22521.50831.1125-0.61640.81210.2716-0.7791-0.1663-0.13670.5279-0.2274-0.00150.48710.04820.35848.558.239417.0194
23.8586-0.5448-4.00910.07920.56924.17030.8173-0.46562.39480.4431-0.25481.1888-0.6715-0.9767-0.70721.00430.23730.10521.1174-0.21051.2918-10.7091.650921.6228
35.124-0.6741-1.93754.59780.66526.3568-0.2163-0.4718-0.54850.1016-0.03030.3038-0.2181-0.23550.31020.17780.0365-0.010.29850.08410.2297-24.60662.473140.8047
45.8499-1.2388-4.41871.09291.3066.7937-0.1084-0.4244-0.2816-0.0040.06880.0964-0.21850.4213-0.09160.212-0.0245-0.04260.20970.04490.2144-7.3369-0.44932.0194
52.17610.2002-1.08811.4123-0.93742.9728-0.54650.44110.1959-1.78110.5344-0.2904-0.20190.11650.25380.9753-0.39750.04350.67750.02380.28165.6319-5.75395.101
62.27760.4015-0.12891.4808-1.1911.7757-0.6840.72710.6766-1.07910.67290.37310.0225-0.23410.09720.5926-0.2114-0.10130.42730.11090.4197-1.04-9.129814.9138
77.8576-0.31815.39694.2425-1.21964.0411-0.5191-0.05410.5542-0.35310.50650.5275-0.5978-0.34470.2170.2968-0.06090.00750.31310.03830.312811.76799.281226.1004
85.52180.68380.36037.71640.24412.03080.03350.0644-0.51870.03380.1052-0.68620.08270.2744-0.11240.1802-0.0415-0.01480.3147-0.0360.287829.02956.484832.0028
96.62763.03144.07353.13982.19542.5704-0.34780.44170.5813-0.10520.22020.6527-0.35750.00350.18640.2674-0.0577-0.00770.24990.04280.361622.074415.344928.4218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 395 through 404 )B395 - 404
2X-RAY DIFFRACTION2chain 'B' and (resid 405 through 413 )B405 - 413
3X-RAY DIFFRACTION3chain 'B' and (resid 414 through 445 )B414 - 445
4X-RAY DIFFRACTION4chain 'B' and (resid 446 through 489 )B446 - 489
5X-RAY DIFFRACTION5chain 'R' and (resid 2 through 28 )R2 - 28
6X-RAY DIFFRACTION6chain 'R' and (resid 29 through 74 )R29 - 74
7X-RAY DIFFRACTION7chain 'R' and (resid 75 through 92 )R75 - 92
8X-RAY DIFFRACTION8chain 'R' and (resid 93 through 134 )R93 - 134
9X-RAY DIFFRACTION9chain 'R' and (resid 135 through 147 )R135 - 147

+
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