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- EMDB-42214: Caenorhabditis elegans Otopetrin 8 (CeOtop8) in pH 5.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-42214
TitleCaenorhabditis elegans Otopetrin 8 (CeOtop8) in pH 5.0
Map data
Sample
  • Complex: CeOTOP8
    • Protein or peptide: Otopetrin-2
KeywordsProton channel / Otop / C.elegans / Otopetrin / MEMBRANE PROTEIN
Function / homologyOtopetrin / Otopetrin / proton channel activity / proton transmembrane transport / membrane / plasma membrane / Otopetrin-2
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsGan N / Jiang Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140892 United States
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1578 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural mechanism of proton conduction in otopetrin proton channel.
Authors: Ninghai Gan / Weizhong Zeng / Yan Han / Qingfeng Chen / Youxing Jiang /
Abstract: The otopetrin (OTOP) proteins were recently characterized as extracellular proton-activated proton channels. Several recent OTOP channel structures demonstrated that the channels form a dimer with ...The otopetrin (OTOP) proteins were recently characterized as extracellular proton-activated proton channels. Several recent OTOP channel structures demonstrated that the channels form a dimer with each subunit adopting a double-barrel architecture. However, the structural mechanisms underlying some basic functional properties of the OTOP channels remain unresolved, including extracellular pH activation, proton conducting pathway, and rapid desensitization. In this study, we performed structural and functional characterization of the Caenorhabditis elegans OTOP8 (CeOTOP8) and mouse OTOP2 (mOTOP2) and illuminated a set of conformational changes related to the proton-conducting process in OTOP. The structures of CeOTOP8 reveal the conformational change at the N-terminal part of TM12 that renders the channel in a transiently proton-transferring state, elucidating an inter-barrel, Glu/His-bridged proton passage within each subunit. The structures of mOTOP2 reveal the conformational change at the N-terminal part of TM6 that exposes the central glutamate to the extracellular solution for protonation. In addition, the structural comparison between CeOTOP8 and mOTOP2, along with the structure-based mutagenesis, demonstrates that an inter-subunit movement at the OTOP channel dimer interface plays a central role in regulating channel activity. Combining the structural information from both channels, we propose a working model describing the multi-step conformational changes during the proton conducting process.
History
DepositionOct 5, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42214.png

Downloads & links

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Map

FileDownload / File: emd_42214.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.06336386 - 0.10233619
Average (Standard dev.)0.00022213455 (±0.0043721553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42214_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_42214_half_map_2.map
Projections & Slices
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Sample components

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Entire : CeOTOP8

EntireName: CeOTOP8
Components
  • Complex: CeOTOP8
    • Protein or peptide: Otopetrin-2

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Supramolecule #1: CeOTOP8

SupramoleculeName: CeOTOP8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Otopetrin-2

MacromoleculeName: Otopetrin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 69.791508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLMVDEQLKI GATPMYSPSH NPIVIADDME KGGSDSDSLP SSPTHHHELY RRPWIHEPRA TNFFVRLITS LYALILTIIS LVVEVSPTW RTDMWLAETI FYISMYGVGI LFFAYCYIFI IYPGPYNQLI SVLRKYKIIK NSEVWFIMQS QHNGEGAGTL Y LRLGALFF ...String:
MLMVDEQLKI GATPMYSPSH NPIVIADDME KGGSDSDSLP SSPTHHHELY RRPWIHEPRA TNFFVRLITS LYALILTIIS LVVEVSPTW RTDMWLAETI FYISMYGVGI LFFAYCYIFI IYPGPYNQLI SVLRKYKIIK NSEVWFIMQS QHNGEGAGTL Y LRLGALFF GSVGIVLFGL ELFLCIENVA CKKVAIAKMI VAIVFTFIQM HFIFCNSKIT VNSSRKIVAF GMMHLISVNL WT WFRFVLA KQEAKAHKKA QLKQTFRKYY SSSSSSSSEE IHELISAVLN STLNNTPATK TMEPVASRLF ALEHFGDVAT FLT TCIVEY SLIGAAIMFI LWKSIGQNNH QQSNSGKRKV KMRIDCSSSS TGLFAGIIFL IGSLVSMGMY TIFESLRNSS GAQL VFGIV DLSLFSIALG ACIIGLWRMR HLQYRLHAHG EVIDEILLII GLIGEILYCA VGIDVFITCR RSADLTVSAL PAFVF VIRM IQVVVQAAFI LTTSRLRCLS KYSMKYKPGK EIITFLLVSN VTLFVFHTFE GMKSSFGFSS KAATQYNYII YAVGPL LVF YRFHSSACLA EIWKHTYSTK SNEYDHEHMS LSDSNLTAIT PISDIKEIPS PQLLKH

UniProtKB: Otopetrin-2

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
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: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41311
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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