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- EMDB-9134: Human TRPM2 ion channel in a calcium- and ADPR-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-9134
TitleHuman TRPM2 ion channel in a calcium- and ADPR-bound state
Map data
Sample
  • Complex: Human TRPM2 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2
  • Ligand: CALCIUM IONCalcium
Function / homology
Function and homology information


cellular response to purine-containing compound / response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / ligand-gated calcium channel activity / dendritic cell differentiation / cellular response to temperature stimulus / regulation of filopodium assembly / sodium channel activity ...cellular response to purine-containing compound / response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / ligand-gated calcium channel activity / dendritic cell differentiation / cellular response to temperature stimulus / regulation of filopodium assembly / sodium channel activity / calcium ion transmembrane import into cytosol / TRP channels / estrous cycle / regulation of actin cytoskeleton reorganization / response to hydroperoxide / dendritic cell chemotaxis / positive regulation of oxidative stress-induced neuron death / cation transmembrane transport / temperature homeostasis / calcium-release channel activity / calcium ion import across plasma membrane / ficolin-1-rich granule membrane / tertiary granule membrane / calcium-mediated signaling using intracellular calcium source / release of sequestered calcium ion into cytosol / positive regulation of insulin secretion / specific granule membrane / cation channel activity / cellular response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / cytoplasmic vesicle membrane / cellular response to hydrogen peroxide / perikaryon / response to heat / lysosomal membrane / protein homotetramerization / lysosome / neuron projection / Neutrophil degranulation / calcium ion binding / integral component of plasma membrane / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily M member 2 / TRPM, SLOG domain / SLOG in TRPM / NUDIX hydrolase domain / Nudix hydrolase domain profile. / 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: 6.36 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: 2.77
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.77
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9134.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.)
1.07 Å/pix.
x 300 pix.
= 321. Å
1.07 Å/pix.
x 300 pix.
= 321. Å
1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 2.77 / Movie #1: 2.77
Minimum - Maximum-13.418454000000001 - 21.981209
Average (Standard dev.)-0.000000000000725 (±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-13.41821.981-0.000

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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
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Human TRPM2 ion channel

SupramoleculeName: Human TRPM2 ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
PDB model - PDB ID:
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: RELION 2.0
Final angle assignmentType: RANDOM ASSIGNMENT / Details: cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14199

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