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- EMDB-31482: Cryo-EM structure of the human TACAN channel in a closed state -

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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


protein heterooligomerization / nuclear inner membrane / fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transmembrane transport / protein homooligomerization / monoatomic ion channel activity / membrane / plasma membrane
Similarity search - Function
Ion channel TACAN/TMEM120B / TMPIT-like protein
Similarity search - Domain/homology
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

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Structure visualization

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

emd_31482.png

Downloads & links

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Map

FileDownload / File: emd_31482.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Voxel sizeX=Y=Z: 1.014 Å
Density
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

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Supplemental data

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Sample components

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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

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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)

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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: Ion channel TACAN

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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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

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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

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