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- PDB-8srf: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8srf | |||||||||||||||
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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 | |||||||||||||||
![]() | TRPM2 chanzyme | |||||||||||||||
![]() | MEMBRANE PROTEIN / TRPM2 Chanzyme / Channel-enzyme | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 861.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 133.9 KB | Display | |
Data in CIF | ![]() | 206.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40729MC ![]() 8srdC ![]() 8sreC ![]() 8srgC ![]() 8srhC ![]() 8sriC ![]() 8srjC ![]() 8srkC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/RP5.gif)
![](data/chem/img/RP5.gif)
#1: Protein | Mass: 168252.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-RP5 / |
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-Non-polymers , 5 types, 45 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/APR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/APR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-AMP / #4: Chemical | ChemComp-APR / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-CLR / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | 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 / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 900 nm |
Image recording | Average exposure time: 0.02 sec. / Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Version: 1.20.1_4487 / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1761 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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