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- EMDB-9133: Human TRPM2 ion channel in an ADPR-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-9133
TitleHuman TRPM2 ion channel in an ADPR-bound state
Map data
Sample
  • Complex: Human TRPM2 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2
Function / homology
Function and homology information


cellular response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / dendritic cell differentiation / ligand-gated calcium channel activity / response to purine-containing compound / cellular response to temperature stimulus / regulation of filopodium assembly / sodium channel activity ...cellular response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / dendritic cell differentiation / ligand-gated calcium channel activity / response to purine-containing compound / cellular response to temperature stimulus / regulation of filopodium assembly / sodium channel activity / TRP channels / response to hydroperoxide / dendritic cell chemotaxis / calcium ion transmembrane import into cytosol / temperature homeostasis / intracellularly gated calcium channel activity / calcium ion import across plasma membrane / tertiary granule membrane / ficolin-1-rich granule membrane / : / specific granule membrane / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / regulation of actin cytoskeleton organization / calcium ion transmembrane transport / calcium channel activity / cytoplasmic vesicle membrane / cellular response to hydrogen peroxide / calcium ion transport / response to heat / perikaryon / protein homotetramerization / 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: 6.1 Å
AuthorsWang L / Fu TM / Xia S / Wu H
CitationJournal: Science / Year: 2018
Title: Structures and gating mechanism of human TRPM2.
Authors: Longfei Wang / Tian-Min Fu / Yiming Zhou / Shiyu Xia / Anna Greka / Hao Wu /
Abstract: Transient receptor potential (TRP) melastatin 2 (TRPM2) is a cation channel associated with numerous diseases. It has a C-terminal NUDT9 homology (NUDT9H) domain responsible for binding adenosine ...Transient receptor potential (TRP) melastatin 2 (TRPM2) is a cation channel associated with numerous diseases. It has a C-terminal NUDT9 homology (NUDT9H) domain responsible for binding adenosine diphosphate (ADP)-ribose (ADPR), and both ADPR and calcium (Ca) are required for TRPM2 activation. Here we report cryo-electron microscopy structures of human TRPM2 alone, with ADPR, and with ADPR and Ca NUDT9H forms both intra- and intersubunit interactions with the N-terminal TRPM homology region (MHR1/2/3) in the apo state but undergoes conformational changes upon ADPR binding, resulting in rotation of MHR1/2 and disruption of the intersubunit interaction. The binding of Ca further engages transmembrane helices and the conserved TRP helix to cause conformational changes at the MHR arm and the lower gating pore to potentiate channel opening. These findings explain the molecular mechanism of concerted TRPM2 gating by ADPR and Ca and provide insights into the gating mechanism of other TRP channels.
History
DepositionSep 20, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseDec 12, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9133.png

Downloads & links

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Map

FileDownload / File: emd_9133.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 3.6 / Movie #1: 3.6
Minimum - Maximum-14.437989 - 31.379269000000001
Average (Standard dev.)-0.000000000008395 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-14.43831.379-0.000

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Supplemental data

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Sample components

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Entire : Human TRPM2 ion channel

EntireName: Human TRPM2 ion channel
Components
  • Complex: Human TRPM2 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2

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Supramolecule #1: Human TRPM2 ion channel

SupramoleculeName: Human TRPM2 ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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: 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

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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: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.072 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY / Details: 6MIX
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion 2.0
Final angle assignmentType: RANDOM ASSIGNMENT / Details: cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49383

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