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- EMDB-20367: Cryo-EM structure of the zebrafish TRPM2 channel in the apo confo... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20367 | |||||||||
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Title | Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with C4 symmetry | |||||||||
![]() | zebrafish TRPM2 channel in the apo conformation, processed with C4 symmetry | |||||||||
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![]() | warmth sensor / redox sensor / calcium-permeable ion channel / TRP channel / TRPM channel / ion channel / ADP-ribose / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() TRP channels / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / ligand-gated monoatomic cation channel activity / release of sequestered calcium ion into cytosol / calcium ion transmembrane transport / calcium channel activity / monoatomic ion channel activity ...TRP channels / Neutrophil degranulation / ADP-D-ribose binding / mono-ADP-D-ribose binding / ligand-gated calcium channel activity / ligand-gated monoatomic cation channel activity / release of sequestered calcium ion into cytosol / calcium ion transmembrane transport / calcium channel activity / monoatomic ion channel activity / protein homotetramerization / calcium ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Yin Y / Wu M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel. Authors: Ying Yin / Mengyu Wu / Allen L Hsu / William F Borschel / Mario J Borgnia / Gabriel C Lander / Seok-Yong Lee / ![]() Abstract: The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca. The ...The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca. The recently published TRPM2 structures from Danio rerio in the ligand-free and the ADPR/Ca-bound conditions represent the channel in closed and open states, which uncovered substantial tertiary and quaternary conformational rearrangements. However, it is unclear how these rearrangements are achieved within the tetrameric channel during channel gating. Here we report the cryo-electron microscopy structures of Danio rerio TRPM2 in the absence of ligands, in complex with Ca alone, and with both ADPR and Ca, resolved to ~4.3 Å, ~3.8 Å, and ~4.2 Å, respectively. In contrast to the published results, our studies capture ligand-bound TRPM2 structures in two-fold symmetric intermediate states, offering a glimpse of the structural transitions that bridge the closed and open conformations. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 57.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.8 KB 14.8 KB | Display Display | ![]() |
Images | ![]() | 162.9 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pkvMC ![]() 7822C ![]() 6d73C ![]() 6pkwC ![]() 6pkxC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | zebrafish TRPM2 channel in the apo conformation, processed with C4 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.066 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Transient receptor potential cation channel subfamily M member 2
Entire | Name: Transient receptor potential cation channel subfamily M member 2 |
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Components |
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-Supramolecule #1: Transient receptor potential cation channel subfamily M member 2
Supramolecule | Name: Transient receptor potential cation channel subfamily M member 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Transient receptor potential cation channel subfamily M member 2
Macromolecule | Name: Transient receptor potential cation channel subfamily M member 2 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 167.608625 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MALGTSGVKI HPNGNSNQLG VQLENVKLTS LFKKLDKRCS LASWIKENIK KKECCFYVED GREGICKCGY PKVQHCDEAI KPEDYMGEQ WDKHRHVRET PTDAFGDISF GGLGQKTGKY VRVSSDTSCE NLYQLMTEQW KLRSPNLLIS VTGGAKNFYI K THLKDKFR ...String: MALGTSGVKI HPNGNSNQLG VQLENVKLTS LFKKLDKRCS LASWIKENIK KKECCFYVED GREGICKCGY PKVQHCDEAI KPEDYMGEQ WDKHRHVRET PTDAFGDISF GGLGQKTGKY VRVSSDTSCE NLYQLMTEQW KLRSPNLLIS VTGGAKNFYI K THLKDKFR RGLIKVAQTT GAWILTGGTH AGVMKHVGMA VRDYTLSSGS MEGQIVVIGV APWGVIHNRS TLIHPEGRFP AY YSLDEQG QGRLSCLDIN HTHFLLVDDG TQGHYGVEIE LRARLEKLIS KLSLGNRESG VTIPVVCVVL DGGPGTLNTI YNS MLNHTP CVVLEGSGRL ADVIAHVASV PVSKVTMALI NRLLKRFFMQ EYKNFTELQI IEWTKKIQDI LRMPHLLTVF RIDE DKNYD VDVAILQALL KASRSDEHAG RHCWERQLEL AVAWNRVDIA ESEIFTEESQ WTSSDLHPAM FSALVGDKPE FVRLL LENG VCVREFLERE ETLCELYSHL PSCFFLRKLA KRVQGGKMRR GQEPLPGSRK VCLSHVSEEV RHLLGSFTQP LYIASR YKP TKDDVRLKVP SKGALDLPCS GEEWSADTVW DPGRDLFLWA VVQNNRELAE IGWEQCRDCI AAALAASKIL RKLAQES GE DDSEEATEML ELANHYEKQA IGVFSECHSW DAQRAQKLLI RISPSWGRST CLWLALEAHD KSFIAHSGVQ ALLTQIWC G ELSVDNPHWK VLLCMIFFPL IYTGFLTFRR DEDIQRQAER TEQQKLAMES VFAGQSDGKI KRHLRGFSQK SELKPLNCS SRLMSFLKSP QVKFYWNIAS YFGFLWLFAV VLMIDFQTSP SWRELLLYVW LTSLVCEEIR QLYHDFDGSG FRRKAKMYIK DLWNILDVL SIVLFIAGLI CRLQASDTVF YIGKVILCID FIIFCLRLMA IFSISRTLGP KIIIVRRMML DLFFFMFLLS I WVVAYGVA KQGILIENEE RLNWIIRGAV YEPYITIFGN FPTNIDNTLF DISSCSVNAS DPLKPKCPML NADNTPVFPE WL TIMMLCV YLLFANILLL NLLIAIFNYT FQEVQDNTDT IWKFQRYELI KEYHSRPALP PPFILLSHLI LFIRGVFLRD LPQ RHKNFR QELEQTEEEE LLSWEAYMKD NYLASTRQDE SQSVEHRIHD TAEKVGAMSE LLEREQEMV(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)DEEAPHM FARQLQYPDS TVRRFPVPEE KVSWEVNFSP YQPPVYNQQD SSESDTSALD KHRNPGGR T GIRGKGALNT LGPNHILHPI FTRWRDAEHK VLEFLAVWED AEKRWALLGG PAQPDEPLAQ VLERILGKKL NEKTKTLLK AGEEVYKGYV DDSRNTDNAW VETSIITLHC DKNTPLMADL NHMVESSLSS HQPLQWREVS SDACRCSYQR EALRQIAHHH NTYFSNSLE VLFQGPDYKD DDDKAHHHHH HHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.6 mg/mL |
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Buffer | pH: 8 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298.15 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3776 / Average exposure time: 4.6 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 150 |
Output model | ![]() PDB-6pkv: |