[English] 日本語
Yorodumi
- EMDB-7434: Cryo-EM structure of mouse TPC1 channel in the apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7434
TitleCryo-EM structure of mouse TPC1 channel in the apo state
Map dataTPC1 channel in the apo state
Sample
  • Organelle or cellular component: Apo mouse TPC1
    • Protein or peptide: Two pore calcium channel protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
Function / homology
Function and homology information


voltage-gated channel activity / endolysosome / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / Stimuli-sensing channels / phosphatidylinositol-3,5-bisphosphate binding / voltage-gated sodium channel activity / syntaxin binding / monoatomic ion channel complex ...voltage-gated channel activity / endolysosome / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / ligand-gated sodium channel activity / NAADP-sensitive calcium-release channel activity / Stimuli-sensing channels / phosphatidylinositol-3,5-bisphosphate binding / voltage-gated sodium channel activity / syntaxin binding / monoatomic ion channel complex / sodium ion transmembrane transport / positive regulation of autophagy / endocytosis involved in viral entry into host cell / recycling endosome membrane / early endosome membrane / endosome membrane / lysosomal membrane / protein homodimerization activity / membrane
Similarity search - Function
Two pore channel protein 1 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Two pore calcium channel protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShe J / Guo J / Chen Q / Bai X / Jiang Y
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM079179 United States
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1578 United States
Virginia Murchison Linthicum Scholar in Medical Research fund United States
Cancer Prevention and Research Institute of Texas (CPRIT) United States
CitationJournal: Nature / Year: 2018
Title: Structural insights into the voltage and phospholipid activation of the mammalian TPC1 channel.
Authors: Ji She / Jiangtao Guo / Qingfeng Chen / Weizhong Zeng / Youxing Jiang / Xiao-Chen Bai /
Abstract: The organellar two-pore channel (TPC) functions as a homodimer, in which each subunit contains two homologous Shaker-like six-transmembrane (6-TM)-domain repeats. TPCs belong to the voltage-gated ion ...The organellar two-pore channel (TPC) functions as a homodimer, in which each subunit contains two homologous Shaker-like six-transmembrane (6-TM)-domain repeats. TPCs belong to the voltage-gated ion channel superfamily and are ubiquitously expressed in animals and plants. Mammalian TPC1 and TPC2 are localized at the endolysosomal membrane, and have critical roles in regulating the physiological functions of these acidic organelles. Here we present electron cryo-microscopy structures of mouse TPC1 (MmTPC1)-a voltage-dependent, phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P)-activated Na-selective channel-in both the apo closed state and ligand-bound open state. Combined with functional analysis, these structures provide comprehensive structural insights into the selectivity and gating mechanisms of mammalian TPC channels. The channel has a coin-slot-shaped ion pathway in the filter that defines the selectivity of mammalian TPCs. Only the voltage-sensing domain from the second 6-TM domain confers voltage dependence on MmTPC1. Endolysosome-specific PtdIns(3,5)P binds to the first 6-TM domain and activates the channel under conditions of depolarizing membrane potential. Structural comparisons between the apo and PtdIns(3,5)P-bound structures show the interplay between voltage and ligand in channel activation. These MmTPC1 structures reveal lipid binding and regulation in a 6-TM voltage-gated channel, which is of interest in light of the emerging recognition of the importance of phosphoinositide regulation of ion channels.
History
DepositionJan 25, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseApr 4, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6c96
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7434.png

Downloads & links

-
Map

FileDownload / File: emd_7434.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTPC1 channel in the apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0392 / Movie #1: 0.04
Minimum - Maximum-0.0910889 - 0.17749971
Average (Standard dev.)0.0004453338 (±0.0068317465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z256.800256.800256.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0910.1770.000

-
Supplemental data

-
Sample components

-
Entire : Apo mouse TPC1

EntireName: Apo mouse TPC1
Components
  • Organelle or cellular component: Apo mouse TPC1
    • Protein or peptide: Two pore calcium channel protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION

-
Supramolecule #1: Apo mouse TPC1

SupramoleculeName: Apo mouse TPC1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pEZT-BM

-
Macromolecule #1: Two pore calcium channel protein 1

MacromoleculeName: Two pore calcium channel protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 95.414758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVSLDDDVP LILTLDEAES APLPPSNSLG QEQLPSKNGG SHSIHNSQVP SLVSGADSPP SSPTGHNWEM NYQEAAIYLQ EGQNNDKFF THPKDARALA AYLFVHNHFF YMMELLTALL LLLLSLCESP AVPVLKLHTY VHATLELFAL MVVVFELCMK L RWLGFHTF ...String:
MAVSLDDDVP LILTLDEAES APLPPSNSLG QEQLPSKNGG SHSIHNSQVP SLVSGADSPP SSPTGHNWEM NYQEAAIYLQ EGQNNDKFF THPKDARALA AYLFVHNHFF YMMELLTALL LLLLSLCESP AVPVLKLHTY VHATLELFAL MVVVFELCMK L RWLGFHTF VRHKRTMVKT SVLVVQFIEA IVVLVRQTSH VRVTRALRCI FLVDCRYCGG VRRNLRQIFQ SLPPFMDILL LL LFFMIIF AILGFYLFST NPSDPYFSTL ENSIVNLFVL LTTANFPDVM MPSYSRNPWS CVFFIVYLSI ELYFIMNLLL AVV FDTFND IEKHKFKSLL LHKRTAIQHA YGLLASQRRP AGISYRQFEG LMRFYKPRMS ARERFLTFKA LNQSNTPLLS LKDF YDIYE VAALQWKAKR NRQHWFDELP RTAFLIFKGI NILVNSKAFQ YFMYLVVAVN GVWILVETFM LKGGNFTSKH VPWSY LVFL TIYGVELFMK VAGLGPVEYL SSGWNLFDFS VTAFAFLGLL ALTLNMEPFY FIVVLRPLQL LRLFKLKKRY RNVLDT MFE LLPRMASLGL TLLTFYYSFA IVGMEFFNGR LTPNCCNTST VADAYRFINH TVGNKTKVEE GYYYLNNFDN ILNSFVT LF ELTVVNNWYI IMEGVTSQTS HWSRLYFMTF YIVTMVVMTI IVAFILEAFV FRMNYSRKSQ DSEVDSGIVI EKEMSKEE L MAVLELYREE RGTSSDVTRL LDTLSQMEKY QQNSMVFLGR RSRTKSDLSL KMYQEEIQEW YEEHAREQEQ QKLRGSVPG PAAQQPPGSR QRSQTVTVEA GLVPR

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.7 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5e1j

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 42870
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2)
Final 3D classificationSoftware - Name: RELION (ver. 2)

+
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