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- EMDB-7542: Structure of the nvTRPM2 channel in complex with Ca2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-7542
TitleStructure of the nvTRPM2 channel in complex with Ca2+
Map dataStructure of the nvTRPM2 channel in complex with Ca2+
Sample
  • Complex: nvTRPM2 tetramer
    • Protein or peptide: Predicted proteinProtein structure prediction
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CALCIUM IONCalcium
  • Ligand: SODIUM IONSodium
Function / homology
Function and homology information


ligand-gated sodium channel activity / ADP-ribose diphosphatase activity / ligand-gated calcium channel activity / monoatomic cation transmembrane transport / plasma membrane => GO:0005886 / sodium ion transmembrane transport / monoatomic cation channel activity / calcium ion transmembrane transport / metal ion binding / plasma membrane
Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / NUDIX domain / 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-like 2
Similarity search - Component
Biological speciesNematostella vectensis (starlet sea anemone)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsZhang Z / Toth B / Szollosi A / Chen J / Csanady L
Funding support United States, 2 items
OrganizationGrant numberCountry
The Rockefeller University United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Structure of a TRPM2 channel in complex with Ca explains unique gating regulation.
Authors: Zhe Zhang / Balázs Tóth / Andras Szollosi / Jue Chen / László Csanády /
Abstract: Transient receptor potential melastatin 2 (TRPM2) is a Ca-permeable cation channel required for immune cell activation, insulin secretion, and body heat control. TRPM2 is activated by cytosolic Ca, ...Transient receptor potential melastatin 2 (TRPM2) is a Ca-permeable cation channel required for immune cell activation, insulin secretion, and body heat control. TRPM2 is activated by cytosolic Ca, phosphatidyl-inositol-4,5-bisphosphate and ADP ribose. Here, we present the ~3 Å resolution electron cryo-microscopic structure of TRPM2 from , 63% similar in sequence to human TRPM2, in the Ca-bound closed state. Compared to other TRPM channels, TRPM2 exhibits unique structural features that correlate with its function. The pore is larger and more negatively charged, consistent with its high Ca selectivity and larger conductance. The intracellular Ca binding sites are connected to the pore and cytosol, explaining the unusual dependence of TRPM2 activity on intra- and extracellular Ca. In addition, the absence of a post-filter motif is likely the cause of the rapid inactivation of human TRPM2. Together, our cryo-EM and electrophysiology studies provide a molecular understanding of the unique gating mechanism of TRPM2.
History
DepositionMar 12, 2018-
Header (metadata) releaseMar 28, 2018-
Map releaseMay 16, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6co7
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7542.png

Downloads & links

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Map

FileDownload / File: emd_7542.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the nvTRPM2 channel in complex with Ca2+
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.15761204 - 0.2661838
Average (Standard dev.)0.00004233945 (±0.007584064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z395.520395.520395.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-2216-4
NX/NY/NZ376362
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1580.2660.000

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Supplemental data

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Sample components

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Entire : nvTRPM2 tetramer

EntireName: nvTRPM2 tetramer
Components
  • Complex: nvTRPM2 tetramer
    • Protein or peptide: Predicted proteinProtein structure prediction
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CALCIUM IONCalcium
  • Ligand: SODIUM IONSodium

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Supramolecule #1: nvTRPM2 tetramer

SupramoleculeName: nvTRPM2 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nematostella vectensis (starlet sea anemone)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Predicted protein

MacromoleculeName: Predicted protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nematostella vectensis (starlet sea anemone)
Molecular weightTheoretical: 176.663438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGKDSFTPLY DGGDSSHVHL NKFGSNQLSQ SKKSWIARNF SRRECIRFVP KSHDVSRCKC GRPRERHSQQ ALESGQGSEE WNVASCTTK HPTNAYGEID FEGYGGQKRA PYLRMSHDTD ANLVITLMLK RWNLEIPNLV ISVTGGAKSF VLKPRLREMF R RGLIKAAK ...String:
MGKDSFTPLY DGGDSSHVHL NKFGSNQLSQ SKKSWIARNF SRRECIRFVP KSHDVSRCKC GRPRERHSQQ ALESGQGSEE WNVASCTTK HPTNAYGEID FEGYGGQKRA PYLRMSHDTD ANLVITLMLK RWNLEIPNLV ISVTGGAKSF VLKPRLREMF R RGLIKAAK TTGAWIITGG TNTGVMKHVG EAVKEQQLMF GSDTQVNVIG IATWGIVDKQ SDLISEKNGK YPALYSMEPT PG HQGAMLD PNHSHFFLVD DGTEGKYGVE IGMRSRIEEA IMKVKTDSRS EAGSIGVPVV LLVLEGGPNT VATMYELIKK KVP AVVIDG SGRAASVVGF AYNHTIKRNV DGQTINVIDP QYEDEVRAKV VEVFGAKGAD KTYSMIKDVL EDEKMISVYS LDGE ISQDI DLAILKALLK ANRSSPVAQL NLALAWNRID LAKSDIFTEE QQWTTETLSA AMLTALLDDK AEFAELFLQN GLSMR EFLS LDILCKLYAE VPGNTTIKPL LQKEMGKRQV KTIDMDVVGE VIEELMGDMF ESYYRKDGHY FGELASYAEG LVLKNR KSS KDLLANINRI DPLPTPYLDV FLWAVLCNRR ELARVLWEAG REPMAAALMA SRLLKRMASR AQEDNTITDI SSDLYDH AR LFEERAVGVL DECFNENETL SQTLLVRELD HYSRMTALEL AVSAESQDFI AHTSCQVLLT RLWMGTMAMN TRWWKVLV C LYLPVLIFPI IYFVPDEQHE RQAAEREHQK SLNQKSSKVK SHKEKNDAPV VPVYRSKEEK AVSNDEEARV GTENEEEDF QLEDYIPEIR EDDSMEVIMR NKKLGFCDRI MHFYSAPFSK FVGNVVGYLA FIFLYAYVVL FNFPRFDPAK TLGGIHPTEI VLYFWVFTI LIEEIRQLAA KPPKYIKDKV SVYFSDTWNF VDIFSLTVFI IAIILRFFTN SRIFTASRII LSLDIIFFIV R SLQIFSVN RLLGPKLVMI QKMMQDLAQF IIILAVFTIA YGIALHAVMF PSPGIYARNN TWVTITSVVQ YPYWQMYGEL FL DEIQGEK PKEFGEVDPD GRWLSPLLLA IYMVFTNILL LNLLIAIFNY TFERVQEDSD KVWKFQRYDL VQEYHSRPVF APP LVLLGH ILIFIRWVWR MCRCGHPPRG STMKIGLSPA EMEQMDNWEF QAAEMYIHQQ QQKNSGTLEE RVRALGDRVD CINS QLNRV LDSMSGTRAH ALTDGNGLEG GHDSEGRLAR MEVELSSNSE SLQKILALLQ QQPPVKGQAA VPIQLTLLHY KARSS PYPG STAKRFAVQD NMVDWQVPFP DYKPVNYTAP VVLANPVWAD KDLMAMSPRP ELPYNQMDHT CNVNRVSYNG TYVVKD GLP LNPMGRTGMQ GRGLLGRFGP NHAADPVVTR WKRTSAGVML QGGKKVLEFV AIQRKDNNQW AIPGGMVEPG QLVTQAL KA EFGEEAMAKL NVSQEEKERI AKQIERLFQQ GQEIYKGYVD DPRNTDNAWM ETVAVNFHDD KGDLFGDITL QAGDDAAA V RWQRVSGNIP LYASHVSILE KVAKMRDAAF SNSLEVLFQ

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 4 / Number of copies: 56 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 3
Molecular weightTheoretical: 22.99 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

Concentration5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 0.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 1550 / Average exposure time: 0.2 sec. / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 196198
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 104268

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6co7:
Structure of the nvTRPM2 channel in complex with Ca2+

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