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- EMDB-8901: Ion channel receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-8901
TitleIon channel receptor
Map dataIon channel receptor
Sample
  • Complex: Ion channel 1
    • Protein or peptide: Transient receptor potential cation channel, subfamily M, member 2
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


TRP channels / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / ligand-gated monoatomic cation channel activity / monoatomic ion channel activity / calcium ion transmembrane transport / calcium channel activity / protein homotetramerization ...TRP channels / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / ligand-gated monoatomic cation channel activity / monoatomic ion channel activity / calcium ion transmembrane transport / calcium 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: 3.8 Å
AuthorsDu J / Lu 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 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

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

emd_8901.png

Downloads & links

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Map

FileDownload / File: emd_8901.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIon channel receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 322.2 Å		1.07 Å/pix.
x 300 pix.
= 322.2 Å		1.07 Å/pix.
x 300 pix.
= 322.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-9.03637 - 18.386251000000001
Average (Standard dev.)0.037447702 (±0.67021376)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-9.03618.3860.037

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Supplemental data

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Sample components

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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

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Supramolecule #1: Ion channel 1

SupramoleculeName: Ion channel 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 500 KDa

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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: 168.730797 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 EQQKLAMESV FAGQSDGKIK RHLRGFSQKS ELKPLNCSS RLMSFLKSPQ VKFYWNIASY FGFLWLFAVV LMIDFQTSPS WRELLLYVWL TSLVCEEIRQ LYHDFDGSGF RRKAKMYIKD LWNILDVLS IVLFIAGLIC RLQASDTVFY IGKVILCIDF IIFCLRLMAI FSISRTLGPK IIIVRRMMLD LFFFMFLLSI W VVAYGVAK QGILIENEER LNWIIRGAVY EPYITIFGNF PTNIDNTLFD ISSCSVNASD PLKPKCPMLN ADNTPVFPEW LT IMMLCVY LLFANILLLN LLIAIFNYTF QEVQDNTDTI WKFQRYELIK EYHSRPALPP PFILLSHLIL FIRGVFLRDL PQR HKNFRQ ELEQTEEEEL LSWEAYMKDN YLASTRQDES QSVEHRIHDT AEKVGAMSEL LEREQEMVSA TMAKRLARLE EQVS ESAKA LRWIIDALKS QGCKSKVQPP LMRSKSSDRD DGDSSGQETD DEEAPHMFAR QLQYPDSTVR RFPVPEEKVS WEVNF SPYQ PPVYNQQDSS ESDTSALDKH RNPGGRTGIR GKGALNTLGP NHILHPIFTR WRDAEHKVLE FLAVWEDAEK RWALLG GPA QPDEPLAQVL ERILGKKLNE KTKTLLKAGE EVYKGYVDDS RNTDNAWVET SIITLHCDKN TPLMADLNHM VESSLSS HQ PLQWREVSSD ACRCSYQREA LRQIAHHHNT YF

UniProtKB: UNIPROTKB: A0A0R4IN04

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183041
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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