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- EMDB-61215: Structureal mechanism of human TRPM3 ion channel inhibition -

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Basic information

Entry
Database: EMDB / ID: EMD-61215
TitleStructureal mechanism of human TRPM3 ion channel inhibition
Map data
Sample
  • Complex: human TRPM3 ion channel
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
  • Ligand: ~{N}-[(3~{S})-3-(hydroxymethyl)piperidin-3-yl]-6-[(4-methyl-1,3-thiazol-5-yl)methoxy]-2,3-dihydro-1,4-benzoxazine-4-carboxamide
KeywordsTransient receptor potential cation channel / subfamily M / member 3 / MEMBRANE PROTEIN
Function / homology
Function and homology information


metal ion transport / zinc ion transmembrane transport / TRP channels / detection of maltose stimulus / maltose transport complex / carbohydrate transport / monoatomic cation transmembrane transport / carbohydrate transmembrane transporter activity / monoatomic cation transport / maltose binding ...metal ion transport / zinc ion transmembrane transport / TRP channels / detection of maltose stimulus / maltose transport complex / carbohydrate transport / monoatomic cation transmembrane transport / carbohydrate transmembrane transporter activity / monoatomic cation transport / maltose binding / maltose transport / maltodextrin transmembrane transport / monoatomic cation channel activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / phosphatidylinositol-4,5-bisphosphate binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / calcium ion transmembrane transport / calcium channel activity / G-protein beta/gamma-subunit complex binding / outer membrane-bounded periplasmic space / protein homotetramerization / calmodulin binding / periplasmic space / DNA damage response / membrane / plasma membrane
Similarity search - Function
TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Transient receptor potential cation channel subfamily M member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsYang TT / Cheng XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structureal mechanism of human TRPM3 ion channel inhibition
Authors: Yang TT / Cheng XY
History
DepositionAug 20, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61215.png

Downloads & links

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Map

FileDownload / File: emd_61215.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.8752482 - 1.4744854
Average (Standard dev.)0.0027396628 (±0.032498654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61215_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61215_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human TRPM3 ion channel

EntireName: human TRPM3 ion channel
Components
  • Complex: human TRPM3 ion channel
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
  • Ligand: ~{N}-[(3~{S})-3-(hydroxymethyl)piperidin-3-yl]-6-[(4-methyl-1,3-thiazol-5-yl)methoxy]-2,3-dihydro-1,4-benzoxazine-4-carboxamide

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Supramolecule #1: human TRPM3 ion channel

SupramoleculeName: human TRPM3 ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Transient recept...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 183.408453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ATMGMGSSHH HHHHGSSMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN ...String:
ATMGMGSSHH HHHHGSSMKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIFW AHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE IPALDKELKA K GKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKHMNADTDY SIAEAAFNKG ET AMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEAVNKDKPL GAV ALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTNS SSNNNNNNNN NNLG IELEV LFQGPQSEKW SISKHTQLSP TDAFGTIEFQ GGGHSNKAMY VRVSFDTKPD LLLHLMTKEW QLELPKLLIS VHGGL QNFE LQPKLKQVFG KGLIKAAMTT GAWIFTGGVN TGVIRHVGDA LKDHASKSRG KICTIGIAPW GIVENQEDLI GRDVVR PYQ TMSNPMSKLT VLNSMHSHFI LADNGTTGKY GAEVKLRRQL EKHISLQKIN TRCLPFFSLD SRLFYSFWGS CQLDSVG IG QGVPVVALIV EGGPNVISIV LEYLRDTPPV PVVVCDGSGR ASDILAFGHK YSEEGGLINE SLRDQLLVTI QKTFTYTR T QAQHLFIILM ECMKKKELIT VFRMGSEGHQ DIDLAILTAL LKGANASAPD QLSLALAWNR VDIARSQIFI YGQQWPVGS LEQAMLDALV LDRVDFVKLL IENGVSMHRF LTISRLEELY NTRHGPSNTL YHLVRDVKKG NLPPDYRISL IDIGLVIEYL MGGAYRCNY TRKRFRTLYH NLFGPKRPKA LKLLGMEDDI PLRRGRKTTK KREEEVDIDL DDPEINHFPF PFHELMVWAV L MKRQKMAL FFWQHGEEAM AKALVACKLC KAMAHEASEN DMVDDISQEL NHNSRDFGQL AVELLDQSYK QDEQLAMKLL TY ELKNWSN ATCLQLAVAA KHRDFIAHTC SQMLLTDMWM GRLRMRKNSG LKVILGILLP PSILSLEFKN KDDMPYMSQA QEI HLQEKE AEEPEKPTKE KEEEDMELTA MLGRNNGESS RKKDEEEVQS KHRLIPLGRK IYEFYNAPIV KFWFYTLAYI GYLM LFNYI VLVKMERWPS TQEWIVISYI FTLGIEKMRE ILMSEPGKLL QKVKVWLQEY WNVTDLIAIL LFSVGMILRL QDQPF RSDG RVIYCVNIIY WYIRLLDIFG VNKYLGPYVM MIGKMMIDMM YFVIIMLVVL MSFGVARQAI LFPNEEPSWK LAKNIF YMP YWMIYGEVFA DQIDPPCGQN ETREDGKIIQ LPPCKTGAWI VPAIMACYLL VANILLVNLL IAVFNNTFFE VKSISNQ VW KFQRYQLIMT FHERPVLPPP LIIFSHMTMI FQHLCCRWRK HESDPDERDY GLKLFITDDE LKKVHDFEEQ CIEEYFRE K DDRFNSSNDE RIRVTSERVE NMSMRLEEVN EREHSMKASL QTVDIRLAQL EDLIGRMATA LERLTGLERA ESNKIRSRT SSDCTDAAYI

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Transient receptor potential cation channel subfamily M member 3

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Macromolecule #2: ~{N}-[(3~{S})-3-(hydroxymethyl)piperidin-3-yl]-6-[(4-methyl-1,3-t...

MacromoleculeName: ~{N}-[(3~{S})-3-(hydroxymethyl)piperidin-3-yl]-6-[(4-methyl-1,3-thiazol-5-yl)methoxy]-2,3-dihydro-1,4-benzoxazine-4-carboxamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1EA5
Molecular weightTheoretical: 418.51 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.13 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
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 106477
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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