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Yorodumi- PDB-8srk: Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8srk | |||||||||||||||
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Title | Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in the presence of Ca and ADP-ribose | |||||||||||||||
Components | TRPM2 chanzyme | |||||||||||||||
Keywords | MEMBRANE PROTEIN / TRPM2 Chanzyme / Channel-enzyme | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Salpingoeca rosetta (eukaryote) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.14 Å | |||||||||||||||
Authors | Huang, Y. / Kumar, S. / Lu, W. / Du, J. | |||||||||||||||
Funding support | United States, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8srk.cif.gz | 674.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8srk.ent.gz | 511.4 KB | Display | PDB format |
PDBx/mmJSON format | 8srk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/8srk ftp://data.pdbj.org/pub/pdb/validation_reports/sr/8srk | HTTPS FTP |
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-Related structure data
Related structure data | 40734MC 8srdC 8sreC 8srfC 8srgC 8srhC 8sriC 8srjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 137394.172 Da / Num. of mol.: 4 / Fragment: lacking the NUDT9-H domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Gene: PTSG_05449 / Production host: Homo sapiens (human) / References: UniProt: F2UB89 #2: Chemical | ChemComp-APR / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CLR / 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 |
-Sample preparation
Component | Name: TRPM2 chanzyme without NUDT9-H bound to Calcium and ADPR Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Salpingoeca rosetta (eukaryote) |
Source (recombinant) | Organism: Homo sapiens (human) |
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 |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1100 nm |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 64.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20rc3_4406: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Version: 1.20rc3_4406: / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156178 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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