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- EMDB-42216: Mus musculus Otopetrin 2 (mOTOP2) in pH 8.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-42216
TitleMus musculus Otopetrin 2 (mOTOP2) in pH 8.0
Map data
Sample
  • Complex: mOTOP2
    • Protein or peptide: Proton channel OTOP2
KeywordsProton channel / Otop2 / Otopetrin / Mus musculus / MEMBRANE PROTEIN
Function / homologyOtopetrin / Otopetrin / proton channel activity / proton transmembrane transport / membrane / plasma membrane / Proton channel OTOP2
Function and homology information
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 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-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42216.png

Downloads & links

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Map

FileDownload / File: emd_42216.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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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-0.044188913 - 0.091351494
Average (Standard dev.)0.00016535145 (±0.0033607348)
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_42216_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_42216_half_map_2.map
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Sample components

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Entire : mOTOP2

EntireName: mOTOP2
Components
  • Complex: mOTOP2
    • Protein or peptide: Proton channel OTOP2

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Supramolecule #1: mOTOP2

SupramoleculeName: mOTOP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Proton channel OTOP2

MacromoleculeName: Proton channel OTOP2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 62.643996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSEELVPHPN ESLPGPRASP REVWKKGGRL LSVLLAVNVL LLACTLISGG AFNKVAVYDT DVFALLTTMM LLAALWIVFY LLRTARCPD AVPYRDAHAG PIWLRGGLVL FGICTLVMDV FKTGYYSSFF ECQSAIKILH PIIQAVFVIV QTYFLWISAK D CIHTHLDL ...String:
MSEELVPHPN ESLPGPRASP REVWKKGGRL LSVLLAVNVL LLACTLISGG AFNKVAVYDT DVFALLTTMM LLAALWIVFY LLRTARCPD AVPYRDAHAG PIWLRGGLVL FGICTLVMDV FKTGYYSSFF ECQSAIKILH PIIQAVFVIV QTYFLWISAK D CIHTHLDL TRCGLMFTLA TNLAIWMAAV VDESVHQAHS YSGSHGNTSH TRLNPDSKRA GGAAEEDPCL CSTAICQIFQ QG YFYLYPF NIEYSLFAST MLYVMWKNVG RLLASTHGHG HTPSRVSLFR ETFFAGPVLG LLLFVVGLAV FILYEVQVSG ERG HTRQAL VIYYSFNIVC LGLMTLVSLS GSVIYRFDRR AMDHHKNPTR TLDVALLMGA ALGQYAISYY SIVAVVVGSP RDLQ GALNL SHALLMIAQH TFQNVFIIES LHRGPPGAEP REMPPKEPCQ GITFANLDAI RTLPSCPPTP RLVIPNLESP QEAVA IISA PRCHWRRRCL KDISLFLLLC NVILWIMPAF GARPHFSNTV EVDFYGYSLW AAIVNICLPF GIFYRMHAVS SLLEVY VLS

UniProtKB: Proton channel OTOP2

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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: 8
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: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42662
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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