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Yorodumi- EMDB-40733: Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40733 | |||||||||||||||
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Title | Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in the presence of EDTA, apo state | |||||||||||||||
Map data | Unsharpened consensus map. | |||||||||||||||
Sample |
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Keywords | TRPM2 Chanzyme / Channel-enzyme / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Salpingoeca rosetta (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.74 Å | |||||||||||||||
Authors | Huang Y / Kumar S / Lu W / Du J | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: To Be Published Title: Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution Authors: Huang Y / Lu W / Du J | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40733.map.gz | 75.8 MB | EMDB map data format | |
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Header (meta data) | emd-40733-v30.xml emd-40733.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_40733.png | 105.5 KB | ||
Filedesc metadata | emd-40733.cif.gz | 6.1 KB | ||
Others | emd_40733_half_map_1.map.gz emd_40733_half_map_2.map.gz | 76.4 MB 76.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40733 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40733 | HTTPS FTP |
-Validation report
Summary document | emd_40733_validation.pdf.gz | 858.2 KB | Display | EMDB validaton report |
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Full document | emd_40733_full_validation.pdf.gz | 857.7 KB | Display | |
Data in XML | emd_40733_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_40733_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40733 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40733 | HTTPS FTP |
-Related structure data
Related structure data | 8srjMC 8srdC 8sreC 8srfC 8srgC 8srhC 8sriC 8srkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40733.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened consensus map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Unsharpened consensus half2 map.
File | emd_40733_half_map_1.map | ||||||||||||
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Annotation | Unsharpened consensus half2 map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unsharpened consensus half1 map.
File | emd_40733_half_map_2.map | ||||||||||||
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Annotation | Unsharpened consensus half1 map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TRPM2 chanzyme in the presence of EDTA, apo state
Entire | Name: TRPM2 chanzyme in the presence of EDTA, apo state |
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Components |
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-Supramolecule #1: TRPM2 chanzyme in the presence of EDTA, apo state
Supramolecule | Name: TRPM2 chanzyme in the presence of EDTA, apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Salpingoeca rosetta (eukaryote) |
-Macromolecule #1: TRPM2 chanzyme
Macromolecule | Name: TRPM2 chanzyme / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Salpingoeca rosetta (eukaryote) |
Molecular weight | Theoretical: 137.394172 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MQRARPGELV EVIMFRPTGK ARVSNLDESM AMEFTDLRTR AMSSAAMIRQ SVAAKTLLIE NEDGKGSTRM EVQDFMKRFH MHASEDDKT GSPSTAWGTL RFPTKEATAP YLRLSVNDDP EDALLFVKAM LAQKYGETYD RPSLILSVTG GARNFTLPPR L ETAIAKGL ...String: MQRARPGELV EVIMFRPTGK ARVSNLDESM AMEFTDLRTR AMSSAAMIRQ SVAAKTLLIE NEDGKGSTRM EVQDFMKRFH MHASEDDKT GSPSTAWGTL RFPTKEATAP YLRLSVNDDP EDALLFVKAM LAQKYGETYD RPSLILSVTG GARNFTLPPR L ETAIAKGL RLAAQRTNAW VVTGGTNTGV MKLTGQIMEA LSKTQSHFIP PTIGIATYGV IIGGDDMTRG EPPKIGLEYE MH KKDPPKT TPLDDNHNLF LLVDDGSTNK FGKEIKFRAA FENAAGQAFA APVVTIVVQG GPGTLGTALQ AVRQGTPIVV VDG SGLAAD VLAYAYNFMH NPLTRFKSYT IDDLRQKVAQ TFNPKSSQQL TNLLDSALEC VQDPNLVVVY SLQESGIDEF DDCI LKAIF SSQGKLGNKL KQAMYFDQLD VAKRALSEAS KNGQHNEIAA CINDNLMAAM MHNKPHFVEL YLGFDAKIYE LKPSE EVAK TNITALDELP SFALAIEELY KREAKKPHSH VQRLVSLSNT DVLGRHYRVS TQRGDGTTRR IGRDLANTRA YNVLRM DQI FARLVSKDFS VNRDFTIYDS KYDKVPGIQF RRTAQASHML FLWAICLDRF RMARHFWLIG DQSIINALVA SRILERL ST HRALQGPHLA EERAKMQHNA KKFEELAVGV LGECHGSDSH MASEMLHSKN DMFNKKNAIN IAYDAKSLAF LSHPATQS V INADWYGHLK SVTSFWAVLF AFFFPFFVLP FINFSEDHAE QQVEAPRDFF TDAPRSSHSA NSTTSGAHRL RRKFAKFYS APYTRFISDL LSHFVLCVVT SYFVLDKLED TISAIEWILL VWFVALLLEE LRQMIFCDGI AEYISDTWNR LDLIMITLFF VGFFTHASD PSNQDSKVVS KGIHAFLVVV LWLRFMRYYA LSKNLGPKLI MMMEMMKDVS TFVFLLLIFL IGYGVAAQSL L SPDEDFSS RTFIGVLFRP YFQIYGELFL DDLNSEANCL GDTPFTECSR ETVRMVPFFL AVYILGSNVL LVNLLIAMFN DT YMKVQEA AEDLWRKQNY ELCAEYKDRP FLPAPFILLA HVHMLFMRLL RLCGVHTQEH EKIQDDETKR KITTFEELNT DKF LRRWER ERQEMLEARV KMTNDNVVQA MGMMDQLLEH MISFRFSLDQ QATKIKQEIR DDGLPSTEPT GLVSRTPSQP INRL NSAVA VHGHTAEAA UniProtKB: Nudt9 protein |
-Macromolecule #2: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 12 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.2 sec. / Average electron dose: 64.4 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191126 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8srj: |