[English] 日本語
Yorodumi
- EMDB-31482: Cryo-EM structure of the human TACAN channel in a closed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31482
TitleCryo-EM structure of the human TACAN channel in a closed state
Map dataEM map
Sample
  • Organelle or cellular component: Cryo-EM structure of the human TACAN channel in a closed state
    • Protein or peptide: Ion channel TACAN
  • Ligand: CHOLESTEROL
Keywordsdimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


coenzyme A binding / protein heterooligomerization / nuclear inner membrane / fat cell differentiation / monoatomic ion channel activity / detection of mechanical stimulus involved in sensory perception of pain / antiviral innate immune response / protein homooligomerization / monoatomic ion transmembrane transport / endoplasmic reticulum ...coenzyme A binding / protein heterooligomerization / nuclear inner membrane / fat cell differentiation / monoatomic ion channel activity / detection of mechanical stimulus involved in sensory perception of pain / antiviral innate immune response / protein homooligomerization / monoatomic ion transmembrane transport / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Ion channel TACAN/TMEM120B / TMEM120A/B
Similarity search - Domain/homology
Transmembrane protein 120A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsChen XZ / Wang YJ
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
Citation
Journal: Cell Rep / Year: 2022
Title: Cryo-EM structure of the human TACAN in a closed state.
Authors: Xiaozhe Chen / Yaojie Wang / Yang Li / Xuhang Lu / Jianan Chen / Ming Li / Tianlei Wen / Ning Liu / Shenghai Chang / Xing Zhang / Xue Yang / Yuequan Shen /
Abstract: TACAN is an ion channel-like protein that may be involved in sensing mechanical pain. Here, we present the cryo-electron microscopic structure of human TACAN (hTACAN). hTACAN forms a dimer in which ...TACAN is an ion channel-like protein that may be involved in sensing mechanical pain. Here, we present the cryo-electron microscopic structure of human TACAN (hTACAN). hTACAN forms a dimer in which each protomer consists of a transmembrane globular domain (TMD) containing six helices and an intracellular domain (ICD) containing two helices. Molecular dynamic simulations suggest that each protomer contains a putative ion conduction pore. A single-point mutation of the key residue Met207 greatly increases membrane pressure-activated currents. In addition, each hTACAN subunit binds one cholesterol molecule. Our data show the molecular assembly of hTACAN and suggest that wild-type hTACAN is in a closed state.
#1: Journal: Biorxiv / Year: 2021
Title: Cryo-EM structure of the human TACAN channel in a closed state
Authors: Chen X / Wang Y / Li Y / Lu X / Chen J / Li M / Wen T / Liu N / Chang S / Zhang X / Yang X / Shen Y
History
DepositionJun 25, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7f6v
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31482.png

Downloads & links

-
Map

FileDownload / File: emd_31482.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 230 pix.
= 233.22 Å		1.01 Å/pix.
x 230 pix.
= 233.22 Å		1.01 Å/pix.
x 230 pix.
= 233.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168 / Movie #1: 0.25
Minimum - Maximum-1.1572345 - 1.8234755
Average (Standard dev.)0.0009883553 (±0.047608037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 233.22002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z233.220233.220233.220
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-1.1571.8230.001

-
Supplemental data

-
Sample components

-
Entire : Cryo-EM structure of the human TACAN channel in a closed state

EntireName: Cryo-EM structure of the human TACAN channel in a closed state
Components
  • Organelle or cellular component: Cryo-EM structure of the human TACAN channel in a closed state
    • Protein or peptide: Ion channel TACAN
  • Ligand: CHOLESTEROL

-
Supramolecule #1: Cryo-EM structure of the human TACAN channel in a closed state

SupramoleculeName: Cryo-EM structure of the human TACAN channel in a closed state
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Ion channel TACAN

MacromoleculeName: Ion channel TACAN / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.657156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQPPPPGPLG DCLRDWEDLQ QDFQNIQETH RLYRLKLEEL TKLQNNCTSS ITRQKKRLQE LALALKKCKP SLPAEAEGAA QELENQMKE RQGLFFDMEA YLPKKNGLYL SLVLGNVNVT LLSKQAKFAY KDEYEKFKLY LTIILILISF TCRFLLNSRV T DAAFNFLL ...String:
MQPPPPGPLG DCLRDWEDLQ QDFQNIQETH RLYRLKLEEL TKLQNNCTSS ITRQKKRLQE LALALKKCKP SLPAEAEGAA QELENQMKE RQGLFFDMEA YLPKKNGLYL SLVLGNVNVT LLSKQAKFAY KDEYEKFKLY LTIILILISF TCRFLLNSRV T DAAFNFLL VWYYCTLTIR ESILINNGSR IKGWWVFHHY VSTFLSGVML TWPDGLMYQK FRNQFLSFSM YQSFVQFLQY YY QSGCLYR LRALGERHTM DLTVEGFQSW MWRGLTFLLP FLFFGHFWQL FNALTLFNLA QDPQCKEWQV LMCGFPFLLL FLG NFFTTL RVVHHKFHSQ RHGSKKD

UniProtKB: Transmembrane protein 120A

-
Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: C-flat-2/1 / Material: GOLD / 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: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58843
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7f6v:
Cryo-EM structure of the human TACAN channel in a closed state

+
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