[English] 日本語
Yorodumi
- PDB-5wc5: Structural insights into the potency of SK/IK channel positive mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wc5
TitleStructural insights into the potency of SK/IK channel positive modulators
Components
  • Calmodulin-1
  • 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 / membrane repolarization during atrial cardiac muscle cell action potential / Ca2+ activated K+ channels / calcium-activated potassium channel activity / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / membrane repolarization during atrial cardiac muscle cell action potential / Ca2+ activated K+ channels / calcium-activated potassium channel activity / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / alpha-actinin binding / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / potassium ion transport / Stimuli-sensing channels / cellular response to type II interferon / Z disc / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions
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 / EF-hand ...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 / : / Recoverin; domain 1 / 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
7-fluoro-3-(hydroxyamino)-2H-indol-2-one / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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: 2017
Title: Structural insights into the potency of SK channel positive modulators.
Authors: Nam, Y.W. / Orfali, R. / Liu, T. / Yu, K. / Cui, M. / Wulff, H. / Zhang, M.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,58912
Polymers27,6602
Non-polymers92910
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-1
hetero molecules

B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17824
Polymers55,3214
Non-polymers1,85820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15810 Å2
ΔGint-276 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.994, 66.015, 65.298
Angle α, β, γ (deg.)90.000, 93.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-639-

HOH

21B-657-

HOH

Detailsequilibrium centrifugation

-
Components

-
Protein , 2 types, 2 molecules BR

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


Mass: 11240.293 Da / Num. of mol.: 1 / Mutation: N407A
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-1


Mass: 16420.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23

-
Non-polymers , 5 types, 185 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-AJV / 7-fluoro-3-(hydroxyamino)-2H-indol-2-one


Mass: 180.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5FN2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Litium sulfate monohydrate
PH range: 5.6-5.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.3148 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3148 Å / Relative weight: 1
ReflectionResolution: 2.1→26.76 Å / Num. obs: 18443 / % possible obs: 97.8 % / Redundancy: 6 % / Biso Wilson estimate: 22.77 Å2 / Net I/σ(I): 16.5

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XPREPdata scaling
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHASERphasing
RefinementResolution: 2.3→26.788 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 721 4.97 %
Rwork0.195 13786 -
obs0.1978 14507 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.13 Å2 / Biso mean: 34.7876 Å2 / Biso min: 0.61 Å2
Refinement stepCycle: final / Resolution: 2.3→26.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 51 175 2157
Biso mean--64.97 34.57 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081995
X-RAY DIFFRACTIONf_angle_d1.2162676
X-RAY DIFFRACTIONf_chiral_restr0.049294
X-RAY DIFFRACTIONf_plane_restr0.005344
X-RAY DIFFRACTIONf_dihedral_angle_d8.0861215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.47750.37591270.27282732285999
2.4775-2.72660.32471390.25942764290399
2.7266-3.12060.31141380.21327552893100
3.1206-3.92970.21351400.16672763290399
3.9297-26.79010.19971770.15872772294999
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)
10.7547-1.75330.55874.65490.13893.9874-0.13410.53070.3258-0.22580.14540.1527-0.248-0.024-0.0940.2777-0.06780.02690.23330.05340.17988.11068.507817.2259
20.81140.4094-1.50580.4549-0.88612.8523-0.08590.47780.4806-0.68310.17210.5173-0.0346-0.2-0.09450.65270.0587-0.1880.5769-0.06570.7087-11.29490.094422.4304
32.1081-0.0679-0.3151.5451-0.28911.76240.0446-0.204-0.25270.05460.02190.3674-0.1274-0.1151-0.07170.12140.0538-0.00020.15940.03670.1895-25.99533.210942.0696
42.4633-0.396-1.54830.62910.32962.7678-0.0415-0.0717-0.0637-0.03850.07070.081-0.16690.0633-0.04250.1337-0.006-0.02030.09950.00810.1352-8.1325-0.251432.2623
50.5217-0.11510.0210.07970.30251.7205-0.19320.19350.0903-0.55330.1886-0.1131-0.27260.1432-0.16510.641-0.30750.10110.441-0.07320.20185.517-5.41445.2008
62.49420.50940.03620.58480.37791.8237-0.39430.38560.0582-0.36770.2569-0.00230.0841-0.09920.09070.2091-0.06570.02250.15270.00010.1360.4033-11.011420.1839
70.29650.3875-0.64861.0968-1.13111.5567-0.2160.32540.23340.05590.20960.2264-0.0599-0.2183-0.4420.462-0.3437-0.12560.50660.27120.264-4.0536-5.02057.9371
83.7013-0.49153.67511.3524-0.66385.7964-0.2315-0.28690.2785-0.16570.13370.1073-0.2669-0.61980.05980.1692-0.0340.01350.16910.0180.143412.02239.758626.8597
91.50590.4504-0.25882.80771.55821.64190.3125-0.2375-0.39240.34260.05-0.4040.31470.14-0.22840.1787-0.0256-0.08740.2098-0.00830.313825.76644.019235.4041
103.2501-1.6260.16857.09930.8631.78720.16930.2269-0.8796-0.37330.0737-0.6889-0.00720.3628-0.15860.185-0.08020.02440.2161-0.06380.422232.48466.581926.0194
112.51262.3441.412.21121.09342.8779-0.18440.11050.4086-0.19270.08760.0937-0.33490.0010.05130.1668-0.01010.01660.115-0.02940.212624.156315.960929.8431
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 415 )B405 - 415
3X-RAY DIFFRACTION3chain 'B' and (resid 416 through 445 )B416 - 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 55 )R29 - 55
7X-RAY DIFFRACTION7chain 'R' and (resid 56 through 75 )R56 - 75
8X-RAY DIFFRACTION8chain 'R' and (resid 76 through 92 )R76 - 92
9X-RAY DIFFRACTION9chain 'R' and (resid 93 through 117 )R93 - 117
10X-RAY DIFFRACTION10chain 'R' and (resid 118 through 128 )R118 - 128
11X-RAY DIFFRACTION11chain 'R' and (resid 129 through 147 )R129 - 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