[English] 日本語
Yorodumi
- EMDB-13702: Verruculogen-bound Drosophila Slo channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13702
TitleVerruculogen-bound Drosophila Slo channel
Map dataSharpened using Phenix.Autosharpen
Sample
  • Complex: Slo tetramer
    • Protein or peptide: Isoform J of Calcium-activated potassium channel slowpoke
  • Ligand: Verruculogen
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: CHOLESTEROL
  • Ligand: POTASSIUM ION
KeywordsPotassium transport / BK channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


Sperm Motility And Taxes / negative regulation of neuromuscular synaptic transmission / male courtship behavior, veined wing generated song production / regulation of synaptic assembly at neuromuscular junction / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / circadian behavior / monoatomic ion channel complex / potassium ion transmembrane transport / potassium ion transport ...Sperm Motility And Taxes / negative regulation of neuromuscular synaptic transmission / male courtship behavior, veined wing generated song production / regulation of synaptic assembly at neuromuscular junction / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / circadian behavior / monoatomic ion channel complex / potassium ion transmembrane transport / potassium ion transport / circadian rhythm / postsynaptic membrane / neuron projection / response to xenobiotic stimulus / neuronal cell body / membrane / plasma membrane
Similarity search - Function
: / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / : / Calcium-activated BK potassium channel alpha subunit / Calcium-activated potassium channel slowpoke-like RCK domain / RCK N-terminal domain profile. / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Calcium-activated potassium channel slowpoke
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsRaisch T / Brockmann A
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2021
Title: Small molecule modulation of the Drosophila Slo channel elucidated by cryo-EM.
Authors: Tobias Raisch / Andreas Brockmann / Ulrich Ebbinghaus-Kintscher / Jörg Freigang / Oliver Gutbrod / Jan Kubicek / Barbara Maertens / Oliver Hofnagel / Stefan Raunser /
Abstract: Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca concentrations and are ...Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca concentrations and are important targets for insecticides and antiparasitic drugs. However, it is unknown how these compounds modulate ion translocation and whether there are insect-specific binding pockets. Here, we report structures of Drosophila Slo in the Ca-bound and Ca-free form and in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside. Whereas the architecture and gating mechanism of Slo channels are conserved, potential insect-specific binding pockets exist. Verruculogen inhibits K transport by blocking the Ca-induced activation signal and precludes K from entering the selectivity filter. Emodepside decreases the conductance by suboptimal K coordination and uncouples ion gating from Ca and voltage sensing. Our results expand the mechanistic understanding of Slo regulation and lay the foundation for the rational design of regulators of Slo and other voltage-gated ion channels.
History
DepositionOct 8, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7pxg
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13702.png

Downloads & links

-
Map

FileDownload / File: emd_13702.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened using Phenix.Autosharpen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.7 Å/pix.
x 448 pix.
= 313.6 Å		0.7 Å/pix.
x 448 pix.
= 313.6 Å		0.7 Å/pix.
x 448 pix.
= 313.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-18.229161999999999 - 39.447400000000002
Average (Standard dev.)-0.000000000004372 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 313.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.70.70.7
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z313.600313.600313.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ448448448
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-18.22939.447-0.000

-
Supplemental data

-
Additional map: Sharpened with SPHIRE

Fileemd_13702_additional_1.map
AnnotationSharpened with SPHIRE
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13702_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13702_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Slo tetramer

EntireName: Slo tetramer
Components
  • Complex: Slo tetramer
    • Protein or peptide: Isoform J of Calcium-activated potassium channel slowpoke
  • Ligand: Verruculogen
  • Ligand: CALCIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: CHOLESTEROL
  • Ligand: POTASSIUM ION

-
Supramolecule #1: Slo tetramer

SupramoleculeName: Slo tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
Macromolecule #1: Isoform J of Calcium-activated potassium channel slowpoke

MacromoleculeName: Isoform J of Calcium-activated potassium channel slowpoke
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 130.919094 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASGLIDTNF SSTLANGMSG CDQSTVESLA DDPTDSPFDA DDCLKVRKYW CFLLSSIFTF LAGLLVVLLW RAFAFVCCRK EPDLGPNDP KQKEQKASRN KQEFEGTFMT EAKDWAGELI SGQTTTGRIL VVLVFILSIA SLIIYFVDAS SEEVERCQKW S NNITQQID ...String:
MASGLIDTNF SSTLANGMSG CDQSTVESLA DDPTDSPFDA DDCLKVRKYW CFLLSSIFTF LAGLLVVLLW RAFAFVCCRK EPDLGPNDP KQKEQKASRN KQEFEGTFMT EAKDWAGELI SGQTTTGRIL VVLVFILSIA SLIIYFVDAS SEEVERCQKW S NNITQQID LAFNIFFMVY FFIRFIAASD KLWFMLEMYS FVDYFTIPPS FVSIYLDRTW IGLRFLRALR LMTVPDILQY LN VLKTSSS IRLAQLVSIF ISVWLTAAGI IHLLENSGDP LDFDNAHRLS YWTCVYFLIV TMSTVGYGDV YCETVLGRTF LVF FLLVGL AIFASCIPEI IDLIGTRAKY GGTLKNEKGR RHIVVCGHIT YESVSHFLKD FLHEDREDVD VEVVFLHRKP PDLE LEGLF KRHFTTVEFF QGTIMNPIDL QRVKVHEADA CLVLANKYCQ DPDAEDAANI MRVISIKNYS DDIRVIIQLM QYHNK AYLL NIPSWDWKQG DDVICLAELK LGFIAQSCLA PGFSTMMANL FAMRSFKTSP DMQSWTNDYL RGTGMEMYTE TLSPTF IGI PFAQATELCF SKLKLLLLAI EIKGAEEGAD SKISINPRGA KIQANTQGFF IAQSADEVKR AWFYCKACHE DIKDETL IK KCKCKNLATF RKGVRAVQMV GRASDITRDR EDTNLLNRNV RRPNGTGNGT GGMHHMNNTA AAAAAAAAAG KQVNKVKP T VNVSRQVEGQ VISPSQYNRP TSRSSGTGTQ NQNGGVSLPA GIADDQSKDF DFEKTEMKYD STGMFHWSPA KSLEDCILD RNQAAMTVLN GHVVVCLFAD PDSPLIGLRN LVMPLRASNF HYHELKHVVI VGSVDYIRRE WKMLQNLPKI SVLNGSPLSR ADLRAVNVN LCDMCCILSA KVPSNDDPTL ADKEAILASL NIKAMTFDDT IGVLSQRGPE FDNLSATAGS PIVLQRRGSV Y GANVPMIT ELVNDGNVQF LDQDDDDDPD TELYLTQPFA CGTAFAVSVL DSLMSTTYFN QNALTLIRSL ITGGATPELE LI LAEGAGL RGGYSTVESL SNRDRCRVGQ ISLYDGPLAQ FGECGKYGDL FVAALKSYGM LCIGLYRFRD TSSSCDASSK RYV ITNPPD DFSLLPTDQV FVLMQFDPGL EYKPPAVRAP AGGRGTNTQG SGVGGGGSNK DDNS

UniProtKB: Calcium-activated potassium channel slowpoke

-
Macromolecule #2: Verruculogen

MacromoleculeName: Verruculogen / type: ligand / ID: 2 / Number of copies: 4 / Formula: 8H5
Molecular weightTheoretical: 511.567 Da
Chemical component information

ChemComp-8H5:
Verruculogen / toxin*YM

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...

MacromoleculeName: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 5 / Number of copies: 8 / Formula: 6PL
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-6PL:
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

-
Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 80.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1131410
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.3) / Number images used: 66077
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: SPHIRE (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software: (Name: SPHIRE (ver. 1.3), RELION (ver. 3.1))
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5tj6


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7pxg:
Verruculogen-bound Drosophila Slo channel

+
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