[English] 日本語
Yorodumi
- EMDB-27926: Human TRPM2 ion channel in 1 mM F-dADPR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27926
TitleHuman TRPM2 ion channel in 1 mM F-dADPR
Map data
Sample
  • Complex: Human TRPM2 in 1 mM F-dADPR
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2
  • Ligand: [(2R,3S,5R)-5-(6-amino-8-phenyl-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl [(2R,3S,4S,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)
KeywordsTRPM2 / TRP / ADPR / ADP-ribose / NUDT9H / NUDT9 / calcium / ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / ligand-gated calcium channel activity / zinc ion transmembrane transport / dendritic cell differentiation / response to purine-containing compound / regulation of filopodium assembly / cellular response to temperature stimulus / dendritic cell chemotaxis / response to hydroperoxide ...mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / ligand-gated calcium channel activity / zinc ion transmembrane transport / dendritic cell differentiation / response to purine-containing compound / regulation of filopodium assembly / cellular response to temperature stimulus / dendritic cell chemotaxis / response to hydroperoxide / TRP channels / calcium ion transmembrane import into cytosol / temperature homeostasis / sodium channel activity / intracellularly gated calcium channel activity / tertiary granule membrane / calcium ion import across plasma membrane / ficolin-1-rich granule membrane / monoatomic cation channel activity / specific granule membrane / release of sequestered calcium ion into cytosol / cytoplasmic vesicle membrane / cellular response to calcium ion / cell projection / regulation of actin cytoskeleton organization / calcium ion transmembrane transport / calcium channel activity / cellular response to hydrogen peroxide / calcium ion transport / response to heat / protein homotetramerization / perikaryon / lysosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
TRPM, SLOG domain / : / SLOG in TRPM / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang L / Fu TM / Xia S / Wu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A unified mechanism for human TRPM2 activation, desensitization and inhibition
Authors: Wang L / Fu T-M
History
DepositionAug 23, 2022-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27926.png

Downloads & links

-
Map

FileDownload / File: emd_27926.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.234
Minimum - Maximum-1.2469413 - 2.1625707
Average (Standard dev.)0.0016107343 (±0.07628377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_27926_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27926_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human TRPM2 in 1 mM F-dADPR

EntireName: Human TRPM2 in 1 mM F-dADPR
Components
  • Complex: Human TRPM2 in 1 mM F-dADPR
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2
  • Ligand: [(2R,3S,5R)-5-(6-amino-8-phenyl-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl [(2R,3S,4S,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)

-
Supramolecule #1: Human TRPM2 in 1 mM F-dADPR

SupramoleculeName: Human TRPM2 in 1 mM F-dADPR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Transient receptor potential cation channel subfamily M member 2

MacromoleculeName: Transient receptor potential cation channel subfamily M member 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 171.416188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPSALRKAG SEQEEGFEGL PRRVTDLGMV SNLRRSNSSL FKSWRLQCPF GNNDKQESLS SWIPENIKKK ECVYFVESSK LSDAGKVVC QCGYTHEQHL EEATKPHTFQ GTQWDPKKHV QEMPTDAFGD IVFTGLSQKV KKYVRVSQDT PSSVIYHLMT Q HWGLDVPN ...String:
MEPSALRKAG SEQEEGFEGL PRRVTDLGMV SNLRRSNSSL FKSWRLQCPF GNNDKQESLS SWIPENIKKK ECVYFVESSK LSDAGKVVC QCGYTHEQHL EEATKPHTFQ GTQWDPKKHV QEMPTDAFGD IVFTGLSQKV KKYVRVSQDT PSSVIYHLMT Q HWGLDVPN LLISVTGGAK NFNMKPRLKS IFRRGLVKVA QTTGAWIITG GSHTGVMKQV GEAVRDFSLS SSYKEGELIT IG VATWGTV HRREGLIHPT GSFPAEYILD EDGQGNLTCL DSNHSHFILV DDGTHGQYGV EIPLRTRLEK FISEQTKERG GVA IKIPIV CVVLEGGPGT LHTIDNATTN GTPCVVVEGS GRVADVIAQV ANLPVSDITI SLIQQKLSVF FQEMFETFTE SRIV EWTKK IQDIVRRRQL LTVFREGKDG QQDVDVAILQ ALLKASRSQD HFGHENWDHQ LKLAVAWNRV DIARSEIFMD EWQWK PSDL HPTMTAALIS NKPEFVKLFL ENGVQLKEFV TWDTLLYLYE NLDPSCLFHS KLQKVLVEDP ERPACAPAAP RLQMHH VAQ VLRELLGDFT QPLYPRPRHN DRLRLLLPVP HVKLNVQGVS LRSLYKRSSG HVTFTMDPIR DLLIWAIVQN RRELAGI IW AQSQDCIAAA LACSKILKEL SKEEEDTDSS EEMLALAEEY EHRAIGVFTE CYRKDEERAQ KLLTRVSEAW GKTTCLQL A LEAKDMKFVS HGGIQAFLTK VWWGQLSVDN GLWRVTLCML AFPLLLTGLI SFREKRLQDV GTPAARARAF FTAPVVVFH LNILSYFAFL CLFAYVLMVD FQPVPSWCEC AIYLWLFSLV CEEMRQLFYD PDECGLMKKA ALYFSDFWNK LDVGAILLFV AGLTCRLIP ATLYPGRVIL SLDFILFCLR LMHIFTISKT LGPKIIIVKR MMKDVFFFLF LLAVWVVSFG VAKQAILIHN E RRVDWLFR GAVYHSYLTI FGQIPGYIDG VNFNPEHCSP NGTDPYKPKC PESDATQQRP AFPEWLTVLL LCLYLLFTNI LL LNLLIAM FNYTFQQVQE HTDQIWKFQR HDLIEEYHGR PAAPPPFILL SHLQLFIKRV VLKTPAKRHK QLKNKLEKNE EAA LLSWEI YLKENYLQNR QFQQKQRPEQ KIEDISNKVD AMVDLLDLDP LKRSGSMEQR LASLEEQVAQ TAQALHWIVR TLRA SGFSS EADVPTLASQ KAAEEPDAEP GGRKKTEEPG DSYHVNARHL LYPNCPVTRF PVPNEKVPWE TEFLIYDPPF YTAER KDAA AMDPMGDTLE PLSTIQYNVV DGLRDRRSFH GPYTVQAGLP LNPMGRTGLR GRGSLSCFGP NHTLYPMVTR WRRNED GAI CRKSIKKMLE VLVVKLPLSE HWALPGGSRE PGEMLPRKLK RILRQEHWPS FENLLKCGME VYKGYMDDPR NTDNAWI ET VAVSVHFQDQ NDVELNRLNS NLHACDSGAS IRWQVVDRRI PLYANHKTLL QKAAAEFGAH Y

UniProtKB: Transient receptor potential cation channel subfamily M member 2

-
Macromolecule #2: [(2R,3S,5R)-5-(6-amino-8-phenyl-9H-purin-9-yl)-3-hydroxyoxolan-2-...

MacromoleculeName: [(2R,3S,5R)-5-(6-amino-8-phenyl-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl [(2R,3S,4S,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)
type: ligand / ID: 2 / Number of copies: 8 / Formula: UOZ
Molecular weightTheoretical: 619.412 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

6mix

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61503
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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