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- EMDB-40729: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium,... -
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Open data
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Basic information
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Title | Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium, ADP-ribose, Adenosine monophosphate, and Ribose-5-phosphate, closed state | |||||||||||||||
![]() | Sharpened composite map. | |||||||||||||||
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![]() | TRPM2 Chanzyme / Channel-enzyme / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.52 Å | |||||||||||||||
![]() | Huang Y / Kumar S / Lu W / Du J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 31.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.7 KB 24.7 KB | Display Display | ![]() |
Images | ![]() | 144.7 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 255.4 MB 29 MB 253.2 MB 16.5 MB 256.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8srfMC ![]() 8srdC ![]() 8sreC ![]() 8srgC ![]() 8srhC ![]() 8sriC ![]() 8srjC ![]() 8srkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened composite map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened composite map.
File | emd_40729_additional_1.map | ||||||||||||
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Annotation | Unsharpened composite map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sharpened consensus map.
File | emd_40729_additional_2.map | ||||||||||||
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Annotation | Sharpened consensus map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened consensus map.
File | emd_40729_additional_3.map | ||||||||||||
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Annotation | Unsharpened consensus map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sharpened NUDT9-H focused map.
File | emd_40729_additional_4.map | ||||||||||||
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Annotation | Sharpened NUDT9-H focused map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened NUDT9-H focused map.
File | emd_40729_additional_5.map | ||||||||||||
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Annotation | Unsharpened NUDT9-H focused map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : TRPM2 chanzyme incubated with Magnesium and ADP-ribose for 10s; A...
Entire | Name: TRPM2 chanzyme incubated with Magnesium and ADP-ribose for 10s; ADP-ribose partially hydrolyzed; intact ADP-ribose in MHR1/2 domain; Adenosine monophosphate and Ribose-5-phosphate in NUDT9-H domain; closed state. |
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Components |
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-Supramolecule #1: TRPM2 chanzyme incubated with Magnesium and ADP-ribose for 10s; A...
Supramolecule | Name: TRPM2 chanzyme incubated with Magnesium and ADP-ribose for 10s; ADP-ribose partially hydrolyzed; intact ADP-ribose in MHR1/2 domain; Adenosine monophosphate and Ribose-5-phosphate in NUDT9-H domain; closed state. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 168.252484 KDa |
Recombinant expression | Organism: ![]() |
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 VHGHTAEAAE WYVPPEEYPK SGGVKRYLID ASMVPLSIMC PSYDPVEYTH PSVAAQPVWA DPADPRKIKF NVKDE VNGK VVDRTSCHPS GISIDSNTGR PINPWGRTGM TGRGLLGKWG VNQAADTVVT RWKRSPDGSI LERDGKKVLE FVAIQR QDN KMWAIPGGFV DNGEDVALTS GREFMEEALG MGTSADLMSA ESKDSLAALF SSGTIVARIY CEDPRNTDNA WVETTCV NF HDESGRHAAR LKLQGGDDAE HARWMMVHGG LNLFASHRTL LQHVTSALNA YF UniProtKB: Nudt9 protein |
-Macromolecule #2: 5-O-phosphono-beta-D-ribofuranose
Macromolecule | Name: 5-O-phosphono-beta-D-ribofuranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: RP5 |
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Molecular weight | Theoretical: 230.11 Da |
Chemical component information | ![]() ChemComp-RP5: |
-Macromolecule #3: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ![]() ChemComp-AMP: |
-Macromolecule #4: ADENOSINE-5-DIPHOSPHORIBOSE
Macromolecule | Name: ADENOSINE-5-DIPHOSPHORIBOSE / type: ligand / ID: 4 / Number of copies: 4 / Formula: APR |
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Molecular weight | Theoretical: 559.316 Da |
Chemical component information | ![]() ChemComp-APR: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 21 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 12 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.02 sec. / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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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: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1761 |
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-8srf: |