[English] 日本語
Yorodumi
- EMDB-17197: Human TPC2 in Complex with Antagonist (S)-SG-094 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17197
TitleHuman TPC2 in Complex with Antagonist (S)-SG-094
Map data
Sample
  • Complex: Homodimeric complex of human Two-pore channel 2 (TPC2)
    • Protein or peptide: Two pore channel protein 2
  • Ligand: di-heneicosanoyl phosphatidyl choline
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
  • Ligand: (1S)-6-methoxy-2-methyl-7-phenoxy-1-[(4-phenoxyphenyl)methyl]-3,4-dihydro-1H-isoquinoline
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsTPC2 / two-pore channel / ion channel / inhibitor / homodimer / METAL TRANSPORT
Function / homology
Function and homology information


endosome to lysosome transport of low-density lipoprotein particle / negative regulation of developmental pigmentation / intracellular pH reduction / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / melanosome membrane / regulation of exocytosis / response to vitamin D / endolysosome membrane ...endosome to lysosome transport of low-density lipoprotein particle / negative regulation of developmental pigmentation / intracellular pH reduction / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / melanosome membrane / regulation of exocytosis / response to vitamin D / endolysosome membrane / phosphatidylinositol-3,5-bisphosphate binding / monoatomic ion channel complex / lysosome organization / sodium ion transmembrane transport / smooth muscle contraction / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / monoatomic ion transmembrane transport / regulation of autophagy / calcium-mediated signaling / calcium channel activity / endocytosis involved in viral entry into host cell / Stimuli-sensing channels / intracellular calcium ion homeostasis / late endosome membrane / receptor-mediated endocytosis of virus by host cell / lysosome / endosome membrane / lysosomal membrane / protein kinase binding / identical protein binding / cytosol
Similarity search - Function
Two pore channel protein 2 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Two pore channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChi G / Pike ACW / Maclean EM / Li H / Mukhopadhyay SMM / Bohstedt T / Wang D / McKinley G / Fernandez-Cid A / Duerr K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Structure / Year: 2024
Title: Structural basis for inhibition of the lysosomal two-pore channel TPC2 by a small molecule antagonist.
Authors: Gamma Chi / Dawid Jaślan / Veronika Kudrina / Julia Böck / Huanyu Li / Ashley C W Pike / Susanne Rautenberg / Einar Krogsaeter / Tina Bohstedt / Dong Wang / Gavin McKinley / Alejandra ...Authors: Gamma Chi / Dawid Jaślan / Veronika Kudrina / Julia Böck / Huanyu Li / Ashley C W Pike / Susanne Rautenberg / Einar Krogsaeter / Tina Bohstedt / Dong Wang / Gavin McKinley / Alejandra Fernandez-Cid / Shubhashish M M Mukhopadhyay / Nicola A Burgess-Brown / Marco Keller / Franz Bracher / Christian Grimm / Katharina L Dürr /
Abstract: Two pore channels are lysosomal cation channels with crucial roles in tumor angiogenesis and viral release from endosomes. Inhibition of the two-pore channel 2 (TPC2) has emerged as potential ...Two pore channels are lysosomal cation channels with crucial roles in tumor angiogenesis and viral release from endosomes. Inhibition of the two-pore channel 2 (TPC2) has emerged as potential therapeutic strategy for the treatment of cancers and viral infections, including Ebola and COVID-19. Here, we demonstrate that antagonist SG-094, a synthetic analog of the Chinese alkaloid medicine tetrandrine with increased potency and reduced toxicity, induces asymmetrical structural changes leading to a single binding pocket at only one intersubunit interface within the asymmetrical dimer. Supported by functional characterization of mutants by Ca imaging and patch clamp experiments, we identify key residues in S1 and S4 involved in compound binding to the voltage sensing domain II. SG-094 arrests IIS4 in a downward shifted state which prevents pore opening via the IIS4/S5 linker, hence resembling gating modifiers of canonical VGICs. These findings may guide the rational development of new therapeutics antagonizing TPC2 activity.
History
DepositionApr 24, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17197.png

Downloads & links

-
Map

FileDownload / File: emd_17197.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.829 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.38211802 - 0.6343333
Average (Standard dev.)0.0022395055 (±0.020754337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.7 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17197_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_17197_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17197_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homodimeric complex of human Two-pore channel 2 (TPC2)

EntireName: Homodimeric complex of human Two-pore channel 2 (TPC2)
Components
  • Complex: Homodimeric complex of human Two-pore channel 2 (TPC2)
    • Protein or peptide: Two pore channel protein 2
  • Ligand: di-heneicosanoyl phosphatidyl choline
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
  • Ligand: (1S)-6-methoxy-2-methyl-7-phenoxy-1-[(4-phenoxyphenyl)methyl]-3,4-dihydro-1H-isoquinoline
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: Homodimeric complex of human Two-pore channel 2 (TPC2)

SupramoleculeName: Homodimeric complex of human Two-pore channel 2 (TPC2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

-
Macromolecule #1: Two pore channel protein 2

MacromoleculeName: Two pore channel protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.28543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEPQAESEP AAGGARGGGG DWPAGLTTYR SIQVGPGAAA RWDLCIDQAV VFIEDAIQYR SINHRVDASS MWLYRRYYSN VCQRTLSFT IFLILFLAFI ETPSSLTSTA DVRYRAAPWE PPCGLTESVE VLCLLVFAAD LSVKGYLFGW AHFQKNLWLL G YLVVLVVS ...String:
MAEPQAESEP AAGGARGGGG DWPAGLTTYR SIQVGPGAAA RWDLCIDQAV VFIEDAIQYR SINHRVDASS MWLYRRYYSN VCQRTLSFT IFLILFLAFI ETPSSLTSTA DVRYRAAPWE PPCGLTESVE VLCLLVFAAD LSVKGYLFGW AHFQKNLWLL G YLVVLVVS LVDWTVSLSL VCHEPLRIRR LLRPFFLLQN SSMMKKTLKC IRWSLPEMAS VGLLLAIHLC LFTMFGMLLF AG GKQDDGQ DRERLTYFQN LPESLTSLLV LLTTANNPDV MIPAYSKNRA YAIFFIVFTV IGSLFLMNLL TAIIYSQFRG YLM KSLQTS LFRRRLGTRA AFEVLSSMVG EGGAFPQAVG VKPQNLLQVL QKVQLDSSHK QAMMEKVRSY GSVLLSAEEF QKLF NELDR SVVKEHPPRP EYQSPFLQSA QFLFGHYYFD YLGNLIALAN LVSICVFLVL DADVLPAERD DFILGILNCV FIVYY LLEM LLKVFALGLR GYLSYPSNVF DGLLTVVLLV LEISTLAVYR LPHPGWRPEM VGLLSLWDMT RMLNMLIVFR FLRIIP SMK PMAVVASTVL GLVQNMRAFG GILVVVYYVF AIIGINLFRG VIVALPGNSS LAPANGSAPC GSFEQLEYWA NNFDDFA AA LVTLWNLMVV NNWQVFLDAY RRYSGPWSKI YFVLWWLVSS VIWVNLFLAL ILENFLHKWD PRSHLQPLAG TPEATYQM T VELLFRDILE EPEEDELTER LSQHPHLWLC R

UniProtKB: Two pore channel protein 2

-
Macromolecule #2: di-heneicosanoyl phosphatidyl choline

MacromoleculeName: di-heneicosanoyl phosphatidyl choline / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLD
Molecular weightTheoretical: 875.313 Da
Chemical component information

ChemComp-PLD:
di-heneicosanoyl phosphatidyl choline

-
Macromolecule #3: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...

MacromoleculeName: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
type: ligand / ID: 3 / Number of copies: 3 / Formula: Q7G
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

-
Macromolecule #4: (1S)-6-methoxy-2-methyl-7-phenoxy-1-[(4-phenoxyphenyl)methyl]-3,4...

MacromoleculeName: (1S)-6-methoxy-2-methyl-7-phenoxy-1-[(4-phenoxyphenyl)methyl]-3,4-dihydro-1H-isoquinoline
type: ligand / ID: 4 / Number of copies: 1 / Formula: W4E
Molecular weightTheoretical: 451.556 Da

-
Macromolecule #5: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 5 / Number of copies: 2 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

-
Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 6 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109417
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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