[English] 日本語
Yorodumi
- EMDB-53173: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagoni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53173
TitleCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
Map dataCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
Sample
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
    • Protein or peptide: MKIAA1616 protein
  • Ligand: 1-[2,4-bis(oxidanyl)phenyl]-2-(4-methoxyphenyl)ethanone
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: (25R)-14beta,17beta-spirost-5-en-3beta-ol
KeywordsCa2+ channel Ononetin-bound Closed conformation / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein tetramerization / calcium channel activity / calmodulin binding / 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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsShkumatov AV / Schenck S / Brunner JD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
Authors: Shkumatov AV / Schenck S / Brunner JD
History
DepositionMar 16, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53173.png

Downloads & links

-
Map

FileDownload / File: emd_53173.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of mouse TRPM3 alpha 2 in complex with antagonist Ononetin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 500 pix.
= 346.5 Å		0.69 Å/pix.
x 500 pix.
= 346.5 Å		0.69 Å/pix.
x 500 pix.
= 346.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0189
Minimum - Maximum-0.043415423 - 0.1264662
Average (Standard dev.)0.000023497943 (±0.0034287015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 346.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53173_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Input for consensus map together with main map

Fileemd_53173_additional_1.map
AnnotationInput for consensus map together with main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Consensus map used for model building and phenix validation

Fileemd_53173_additional_2.map
AnnotationConsensus map used for model building and phenix validation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfB

Fileemd_53173_half_map_1.map
AnnotationhalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfA

Fileemd_53173_half_map_2.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin

EntireName: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
Components
  • Complex: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
    • Protein or peptide: MKIAA1616 protein
  • Ligand: 1-[2,4-bis(oxidanyl)phenyl]-2-(4-methoxyphenyl)ethanone
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: (25R)-14beta,17beta-spirost-5-en-3beta-ol

-
Supramolecule #1: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin

SupramoleculeName: Tetrameric assembly of mouse TRPM3 alpha 2 with inhibitor Ononetin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 161 KDa

-
Macromolecule #1: MKIAA1616 protein

MacromoleculeName: MKIAA1616 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 161.96325 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGKKWRDAG ELERGCSDRE DSAESRRRSR SASRGRFAES WKRLSSKQGS TKRSGLPAQQ TPAQKSWIER AFYKRECVHI IPSTKDPHR CCCGRLIGQH VGLTPSISVL QNEKNESRLS RNDIQSEKWS ISKHTQLSPT DAFGTIEFQG GGHSNKAMYV R VSFDTKPD ...String:
MSGKKWRDAG ELERGCSDRE DSAESRRRSR SASRGRFAES WKRLSSKQGS TKRSGLPAQQ TPAQKSWIER AFYKRECVHI IPSTKDPHR CCCGRLIGQH VGLTPSISVL QNEKNESRLS RNDIQSEKWS ISKHTQLSPT DAFGTIEFQG GGHSNKAMYV R VSFDTKPD LLLHLMTKEW QLELPKLLIS VHGGLQNFEL QPKLKQVFGK GLIKAAMTTG AWIFTGGVNT GVIRHVGDAL KD HASKSRG KICTIGIAPW GIVENQEDLI GRDVVRPYQT MSNPMSKLTV LNSMHSHFIL ADNGTTGKYG AEVKLRRQLE KHI SLQKIN TRIGQGVPVV ALIVEGGPNV ISIVLEYLRD TPPVPVVVCD GSGRASDILA FGHKYSEEGG LINESLRDQL LVTI QKTFT YTRTQAQHLF IILMECMKKK ELITVFRMGS EGHQDIDLAI LTALLKGANA SAPDQLSLAL AWNRVDIARS QIFIY GQQW PVGSLEQAML DALVLDRVDF VKLLIENGVS MHRFLTISRL EELYNTRHGP SNTLYHLVRD VKKGNLPPDY RISLID IGL VIEYLMGGAY RCNYTRKRFR TLYHNLFGPK RPKALKLLGM EDDIPLRRGR KTTKKREEEV DIDLDDPEIN HFPFPFH EL MVWAVLMKRQ KMALFFWQHG EEAMAKALVA CKLCKAMAHE ASENDMVDDI SQELNHNSRD FGQLAVELLD QSYKQDEQ L AMKLLTYELK NWSNATCLQL AVAAKHRDFI AHTCSQMLLT DMWMGRLRMR KNSGLKVILG ILLPPSILSL EFKNKDDMP YMTQAQEIHL QEKEPEEPEK PTKEKDEEDM ELTAMLGRSN GESSRKKDEE EVQSRHRLIP VGRKIYEFYN APIVKFWFYT LAYIGYLML FNYIVLVKME RWPSTQEWIV ISYIFTLGIE KMREILMSEP GKLLQKVKVW LQEYWNVTDL IAILLFSVGM I LRLQDQPF RSDGRVIYCV NIIYWYIRLL DIFGVNKYLG PYVMMIGKMM IDMMYFVIIM LVVLMSFGVA RQAILFPNEE PS WKLAKNI FYMPYWMIYG EVFADQIDPP CGQNETREDG KTIQLPPCKT GAWIVPAIMA CYLLVANILL VNLLIAVFNN TFF EVKSIS NQVWKFQRYQ LIMTFHERPV LPPPLIIFSH MTMIFQHVCC RWRKHESDQD ERDYGLKLFI TDDELKKVHD FEEQ CIEEY FREKDDRFNS SNDERIRVTS ERVENMSMRL EEVNEREHSM KASLQTVDIR LAQLEDLIGR MATALERLTG LERAE SNKI RSRTSSDCTD AAYIVRQSSF NSQEGNTFKL QESIDPAGEE TISPTSPTLM PRMRSHSFYS VALEVLFQGP QGTEQK LIS EEDLRGASMD EKTTGWRGGH VVEGLAGELE QLRARLEHHP QGQREP

UniProtKB: Transient receptor potential cation channel subfamily M member 3

-
Macromolecule #2: 1-[2,4-bis(oxidanyl)phenyl]-2-(4-methoxyphenyl)ethanone

MacromoleculeName: 1-[2,4-bis(oxidanyl)phenyl]-2-(4-methoxyphenyl)ethanone
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1D6M
Molecular weightTheoretical: 258.269 Da

-
Macromolecule #3: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

-
Macromolecule #4: (25R)-14beta,17beta-spirost-5-en-3beta-ol

MacromoleculeName: (25R)-14beta,17beta-spirost-5-en-3beta-ol / type: ligand / ID: 4 / Number of copies: 8 / Formula: YUV
Molecular weightTheoretical: 414.621 Da
Chemical component information

ChemComp-YUV:
(25R)-14beta,17beta-spirost-5-en-3beta-ol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H17N2NaO4SHepes
150.0 mMNaClSodium chloride
0.0063 %C56H92O25Glycodiosgenin
10.0 uMC15H14O4Ononetin

Details: 10 mM Hepes pH 7.5, 150 mM NaCl, 0.063% Glycodiosgenin, 10 uM Ononetin
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279.15 K / Instrument: LEICA EM GP / Details: GP2.

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7000000000000001 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dds

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307949
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more