[English] 日本語
Yorodumi
- PDB-9j84: Structureal mechanism of human TRPM3 ion channel inhibition -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j84
TitleStructureal mechanism of human TRPM3 ion channel inhibition
ComponentsMaltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
KeywordsMEMBRANE PROTEIN / Transient receptor potential cation channel / subfamily M / member 3
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 speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsYang, T.T. / Cheng, X.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structureal mechanism of human TRPM3 ion channel inhibition
Authors: Yang, T.T. / Cheng, X.Y.
History
DepositionAug 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
B: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
C: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
D: Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,3088
Polymers733,6344
Non-polymers1,6744
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Transient receptor potential cation channel subfamily M member 3 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Long transient receptor ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Long transient receptor potential channel 3 / LTrpC-3 / LTrpC3 / Melastatin-2 / MLSN2


Mass: 183408.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, TRPM3, KIAA1616, LTRPC3 / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: Q9HCF6
#2: Chemical
ChemComp-A1EA5 / ~{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


Mass: 418.510 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N4O4S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: human TRPM3 ion channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (strain K12) (bacteria)83333
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50.13 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106477 / Symmetry type: POINT

+
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