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Yorodumi- EMDB-7822: Cryo-EM structure of the zebrafish TRPM2 channel in the presence ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7822 | |||||||||
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Title | Cryo-EM structure of the zebrafish TRPM2 channel in the presence of Ca2+ | |||||||||
Map data | Single-particle cryo-EM reconstruction of TRPM2 | |||||||||
Sample |
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Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Yin Y / Wu M / Borschel WF / Lander GC / Lee S-Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7822.map.gz | 113 MB | EMDB map data format | |
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Header (meta data) | emd-7822-v30.xml emd-7822.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7822_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_7822.png | 246.1 KB | ||
Others | emd_7822_half_map_1.map.gz emd_7822_half_map_2.map.gz | 96.4 MB 96.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7822 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7822 | HTTPS FTP |
-Validation report
Summary document | emd_7822_validation.pdf.gz | 776.1 KB | Display | EMDB validaton report |
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Full document | emd_7822_full_validation.pdf.gz | 775.6 KB | Display | |
Data in XML | emd_7822_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_7822_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7822 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7822 | HTTPS FTP |
-Related structure data
Related structure data | 6d73MC 6pkvC 6pkwC 6pkxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7822.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single-particle cryo-EM reconstruction of TRPM2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half 1
File | emd_7822_half_map_1.map | ||||||||||||
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Annotation | Half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half 2
File | emd_7822_half_map_2.map | ||||||||||||
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Annotation | Half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Transient receptor potential cation channel subfamily M member 2 ...
Entire | Name: Transient receptor potential cation channel subfamily M member 2 (TRPM2) |
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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 (TRPM2) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Transient receptor potential cation channel, subfamily M
Macromolecule | Name: Transient receptor potential cation channel, subfamily M type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 167.608625 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-64 / Number real images: 3039 / Average exposure time: 16.0 sec. / Average electron dose: 63.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 100 |
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Output model | PDB-6d73: |