[English] 日本語
Yorodumi
- EMDB-7999: Structure of TRPM2 ion channel receptor by single particle electr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7999
TitleStructure of TRPM2 ion channel receptor by single particle electron cryo-microscopy, ADPR/Ca2+ bound state
Map dataIon channel receptor
Sample
  • Complex: Ion channel 1
    • Protein or peptide: Transient receptor potential cation channel, subfamily M, member 2
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


TRP channels / ligand-gated monoatomic cation channel activity / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / calcium ion transmembrane transport / calcium channel activity / monoatomic ion channel activity / protein homotetramerization ...TRP channels / ligand-gated monoatomic cation channel activity / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / calcium ion transmembrane transport / calcium channel activity / monoatomic ion channel activity / protein homotetramerization / calcium ion binding / plasma membrane
Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / 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 speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDu J / Lu W / Huang Y / Winkler P / Sun W
CitationJournal: Nature / Year: 2018
Title: Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium.
Authors: Yihe Huang / Paige A Winkler / Weinan Sun / Wei Lü / Juan Du /
Abstract: Transient receptor potential melastatin 2 (TRPM2) is a calcium-permeable, non-selective cation channel that has an essential role in diverse physiological processes such as core body temperature ...Transient receptor potential melastatin 2 (TRPM2) is a calcium-permeable, non-selective cation channel that has an essential role in diverse physiological processes such as core body temperature regulation, immune response and apoptosis. TRPM2 is polymodal and can be activated by a wide range of stimuli, including temperature, oxidative stress and NAD-related metabolites such as ADP-ribose (ADPR). Its activation results in both Ca entry across the plasma membrane and Ca release from lysosomes, and has been linked to diseases such as ischaemia-reperfusion injury, bipolar disorder and Alzheimer's disease. Here we report the cryo-electron microscopy structures of the zebrafish TRPM2 in the apo resting (closed) state and in the ADPR/Ca-bound active (open) state, in which the characteristic NUDT9-H domains hang underneath the MHR1/2 domain. We identify an ADPR-binding site located in the bi-lobed structure of the MHR1/2 domain. Our results provide an insight into the mechanism of activation of the TRPM channel family and define a framework for the development of therapeutic agents to treat neurodegenerative diseases and temperature-related pathological conditions.
History
DepositionJun 12, 2018-
Header (metadata) releaseJul 18, 2018-
Map releaseSep 19, 2018-
UpdateOct 17, 2018-
Current statusOct 17, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6drj
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7999.png

Downloads & links

-
Map

FileDownload / File: emd_7999.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIon channel receptor
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 3. / Movie #1: 3
Minimum - Maximum-10.673214 - 21.085353999999999
Average (Standard dev.)0.031051211 (±0.7776872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 322.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z322.200322.200322.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-10.67321.0850.031

-
Supplemental data

-
Sample components

-
Entire : Ion channel 1

EntireName: Ion channel 1
Components
  • Complex: Ion channel 1
    • Protein or peptide: Transient receptor potential cation channel, subfamily M, member 2
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Ion channel 1

SupramoleculeName: Ion channel 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Recombinant expressionOrganism: Mammalia (mammals)
Molecular weightExperimental: 500 KDa

-
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: Danio rerio (zebrafish)
Molecular weightTheoretical: 168.601672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGTSGVKIH PNGNSNQLGV QLENVKLTSL FKKLDKRCSL ASWIKENIKK KECCFYVEDG REGICKCGYP KVQHCDEAIK PEDYMGEQW DKHRHVRETP TDAFGDISFG GLGQKTGKYV RVSSDTSCEN LYQLMTEQWK LRSPNLLISV TGGAKNFYIK T HLKDKFRR ...String:
MLGTSGVKIH PNGNSNQLGV QLENVKLTSL FKKLDKRCSL ASWIKENIKK KECCFYVEDG REGICKCGYP KVQHCDEAIK PEDYMGEQW DKHRHVRETP TDAFGDISFG GLGQKTGKYV RVSSDTSCEN LYQLMTEQWK LRSPNLLISV TGGAKNFYIK T HLKDKFRR GLIKVAQTTG AWILTGGTHA GVMKHVGMAV RDYTLSSGSM EGQIVVIGVA PWGVIHNRST LIHPEGRFPA YY SLDEQGQ GRLSCLDINH THFLLVDDGT QGHYGVEIEL RARLEKLISK LSLGNRESGV TIPVVCVVLD GGPGTLNTIY NSM LNHTPC VVLEGSGRLA DVIAHVASVP VSKVTMALIN RLLKRFFMQE YKNFTELQII EWTKKIQDIL RMPHLLTVFR IDED KNYDV DVAILQALLK ASRSDEHAGR HCWERQLELA VAWNRVDIAE SEIFTEESQW TSSDLHPAMF SALVGDKPEF VRLLL ENGV CVREFLEREE TLCELYSHLP SCFFLRKLAK RVQGGKMRRG QEPLPGSRKV CLSHVSEEVR HLLGSFTQPL YIASRY KPT KDDVRLKVPS KGALDLPCSG EEWSADTVWD PGRDLFLWAV VQNNRELAEI GWEQCRDCIA AALAASKILR KLAQESG ED DSEEATEMLE LANHYEKQAI GVFSECHSWD AQRAQKLLIR ISPSWGRSTC LWLALEAHDK SFIAHSGVQA LLTQIWCG E LSVDNPHWKV LLCMIFFPLI YTGFLTFRRD EDIQRQAERT QQKLAMESVF AGQSDGKIKR HLRGFSQKSE LKPLNCSSR LMSFLKSPQV KFYWNIASYF GFLWLFAVVL MIDFQTSPSW RELLLYVWLT SLVCEEIRQL YHDFDGSGFR RKAKMYIKDL WNILDVLSI VLFIAGLICR LQASDTVFYI GKVILCIDFI IFCLRLMAIF SISRTLGPKI IIVRRMMLDL FFFMFLLSIW V VAYGVAKQ GILIENEERL NWIIRGAVYE PYITIFGNFP TNIDNTLFDI SSCSVNASDP LKPKCPMLNA DNTPVFPEWL TI MMLCVYL LFANILLLNL LIAIFNYTFQ EVQDNTDTIW KFQRYELIKE YHSRPALPPP FILLSHLILF IRGVFLRDLP QRH KNFRQE LEQTEEEELL SWEAYMKDNY LASTRQDESQ SVEHRIHDTA EKVGAMSELL EREQEMVSAT MAKRLARLEE QVSE SAKAL RWIIDALKSQ GCKSKVQPPL MRSKSSDRDD GDSSGQETDD EEAPHMFARQ LQYPDSTVRR FPVPEEKVSW EVNFS PYQP PVYNQQDSSE SDTSALDKHR NPGGRTGIRG KGALNTLGPN HILHPIFTRW RDAEHKVLEF LAVWEDAEKR WALLGG PAQ PDEPLAQVLE RILGKKLNEK TKTLLKAGEE VYKGYVDDSR NTDNAWVETS IITLHCDKNT PLMADLNHMV ESSLSSH QP LQWREVSSDA CRCSYQREAL RQIAHHHNTY F

-
Macromolecule #2: ADENOSINE-5-DIPHOSPHORIBOSE

MacromoleculeName: ADENOSINE-5-DIPHOSPHORIBOSE / type: ligand / ID: 2 / Number of copies: 4 / Formula: APR
Molecular weightTheoretical: 559.316 Da
Chemical component information

ChemComp-APR:
ADENOSINE-5-DIPHOSPHORIBOSE

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227007

+
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