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Yorodumi- PDB-6izf: Structural basis for activity of TRIC counter-ion channels in cal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6izf | |||||||||
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Title | Structural basis for activity of TRIC counter-ion channels in calcium release | |||||||||
Components | Trimeric intracellular cation channel type A | |||||||||
Keywords | MEMBRANE PROTEIN / TRIC / cation channel | |||||||||
Function / homology | TRIC channel / TRIC channel / potassium channel activity / sarcoplasmic reticulum membrane / nuclear membrane / identical protein binding / Chem-BQ9 / Trimeric intracellular cation channel type A Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Wang, X.H. / Zeng, Y. / Su, M. / Hendrickson, W.A. / Chen, Y.H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Structural basis for activity of TRIC counter-ion channels in calcium release. Authors: Wang, X.H. / Su, M. / Gao, F. / Xie, W. / Zeng, Y. / Li, D.L. / Liu, X.L. / Zhao, H. / Qin, L. / Li, F. / Liu, Q. / Clarke, O.B. / Lam, S.M. / Shui, G.H. / Hendrickson, W.A. / Chen, Y.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6izf.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6izf.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 6izf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6izf_validation.pdf.gz | 688 KB | Display | wwPDB validaton report |
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Full document | 6izf_full_validation.pdf.gz | 688.8 KB | Display | |
Data in XML | 6izf_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 6izf_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/6izf ftp://data.pdbj.org/pub/pdb/validation_reports/iz/6izf | HTTPS FTP |
-Related structure data
Related structure data | 6iyuSC 6iyxC 6iyzC 6iz0C 6iz1C 6iz3C 6iz4C 6iz5C 6iz6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36957.551 Da / Num. of mol.: 1 / Mutation: C245S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TMEM38A, RCJMB04_13f15 / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q5ZK43 | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-BQ9 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 21, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.99→48.54 Å / Num. obs: 33712 / % possible obs: 99.6 % / Redundancy: 234.6 % / CC1/2: 1 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.015 / Rrim(I) all: 0.236 / Net I/σ(I): 32.1 / Num. measured all: 7908350 / Scaling rejects: 476 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IYU Resolution: 2→14.992 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.47 Å2 / Biso mean: 52.9376 Å2 / Biso min: 23.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→14.992 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 45.4795 Å / Origin y: 29.4872 Å / Origin z: 43.9823 Å
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Refinement TLS group |
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