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- EMDB-25385: Structure of the human proton-activated chloride channel ASOR in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-25385
TitleStructure of the human proton-activated chloride channel ASOR in desensitized conformation
Map data
Sample
  • Complex: proton activated chloride channel TMEM206 in resting conformation
    • Protein or peptide: Proton-activated chloride channel
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsion channel / chloride channel / MEMBRANE PROTEIN
Function / homologypH-gated chloride channel activity / TMEM206 protein / TMEM206 protein family / chloride transport / chloride channel complex / cell surface / plasma membrane / Proton-activated chloride channel
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLong SB / Wang C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131921 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA008748 United States
CitationJournal: Sci Adv / Year: 2022
Title: Gating choreography and mechanism of the human proton-activated chloride channel ASOR.
Authors: Chongyuan Wang / Maya M Polovitskaya / Bryce D Delgado / Thomas J Jentsch / Stephen B Long /
Abstract: The proton-activated chloride channel ASOR (TMEM206/PAC) permeates anions across cellular membranes in response to acidification, thereby enhancing acid-induced cell death and regulating endocytosis. ...The proton-activated chloride channel ASOR (TMEM206/PAC) permeates anions across cellular membranes in response to acidification, thereby enhancing acid-induced cell death and regulating endocytosis. The molecular mechanisms of pH-dependent control are not understood, in part because structural information for an activated conformation of ASOR is lacking. Here, we reconstitute function from purified protein and present a 3.1-Å-resolution cryo-electron microscopy structure of human ASOR at acidic pH in an activated conformation. The work contextualizes a previous acidic pH structure as a desensitized conformation. Combined with electrophysiological studies and high-resolution structures of resting and desensitized states, the work reveals mechanisms of proton sensing and ion pore gating. Clusters of extracellular acidic residues function as pH sensors and coalesce when protonated. Ensuing conformational changes induce metamorphosis of transmembrane helices to fashion an ion conduction pathway unique to the activated conformation. The studies identify a new paradigm of channel gating in this ubiquitous ion channel.
History
DepositionNov 5, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sqh
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25385.png

Downloads & links

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Map

FileDownload / File: emd_25385.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.2 Å		0.83 Å/pix.
x 384 pix.
= 319.2 Å		0.83 Å/pix.
x 384 pix.
= 319.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.029308524 - 1.1014988
Average (Standard dev.)0.00035407726 (±0.01118633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.831250.831250.83125
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z319.200319.200319.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0291.1010.000

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Supplemental data

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Sample components

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Entire : proton activated chloride channel TMEM206 in resting conformation

EntireName: proton activated chloride channel TMEM206 in resting conformation
Components
  • Complex: proton activated chloride channel TMEM206 in resting conformation
    • Protein or peptide: Proton-activated chloride channel
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: proton activated chloride channel TMEM206 in resting conformation

SupramoleculeName: proton activated chloride channel TMEM206 in resting conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Proton-activated chloride channel

MacromoleculeName: Proton-activated chloride channel / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.092047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRQERSTSY QELSEELVQV VENSELADEQ DKETVRVQGP GILPGLDSES ASSSIRFSKA CLKNVFSVLL IFIYLLLMAV AVFLVYRTI TDFREKLKHP VMSVSYKEVD RYDAPGIALY PGQAQLLSCK HHYEVIPPLT SPGQPGDMNC TTQRINYTDP F SNQTVKSA ...String:
MIRQERSTSY QELSEELVQV VENSELADEQ DKETVRVQGP GILPGLDSES ASSSIRFSKA CLKNVFSVLL IFIYLLLMAV AVFLVYRTI TDFREKLKHP VMSVSYKEVD RYDAPGIALY PGQAQLLSCK HHYEVIPPLT SPGQPGDMNC TTQRINYTDP F SNQTVKSA LIVQGPREVK KRELVFLQFR LNKSSEDFSA IDYLLFSSFQ EFLQSPNRVG FMQACESAYS SWKFSGGFRT WV KMSLVKT KEEDGREAVE FRQETSVVNY IDQRPAAKKS AQLFFVVFEW KDPFIQKVQD IVTANPWNTI ALLCGAFLAL FKA AEFAKL SIKWMIKIRK RYLKRRGQAT SHIS

UniProtKB: Proton-activated chloride channel

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 21 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.6 mg/mL
BufferpH: 4.5
Component:
ConcentrationNameFormula
5.0 mMHEPES
150.0 mMsodium chlorideNaCl
50.0 mMcitrate
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot, blot force of 0.
DetailsMonodisperse sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 157906 / Average exposure time: 4.0 sec. / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 22500
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

Particle selectionNumber selected: 3097510
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model created using CryoSPARC v3.1.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.1.0) / Number images used: 157906
Initial angle assignmentType: RANDOM ASSIGNMENT
Software: (Name: cryoSPARC (ver. v3.1.0), RELION (ver. 3.1))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.1.0)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. v3.1.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 30 / Target criteria: Correlation coefficient
Output model

PDB-7sqh:
Structure of the human proton-activated chloride channel ASOR in desensitized conformation

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