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Yorodumi- PDB-7rxq: Crystal structure of junctophilin-2 in complex with a CaV1.1 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rxq | ||||||
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Title | Crystal structure of junctophilin-2 in complex with a CaV1.1 peptide | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / complex / membrane / ion channel | ||||||
Function / homology | Function and homology information regulation of cardiac muscle tissue development / junctional membrane complex / positive regulation of muscle contraction / junctional sarcoplasmic reticulum membrane / phosphatidylinositol-5-phosphate binding / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / phosphatidic acid binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding ...regulation of cardiac muscle tissue development / junctional membrane complex / positive regulation of muscle contraction / junctional sarcoplasmic reticulum membrane / phosphatidylinositol-5-phosphate binding / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / phosphatidic acid binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / calcium ion transport into cytosol / positive regulation of ryanodine-sensitive calcium-release channel activity / cellular response to caffeine / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / calcium ion import across plasma membrane / voltage-gated calcium channel activity / calcium ion homeostasis / core promoter sequence-specific DNA binding / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / T-tubule / phosphatidylinositol-4,5-bisphosphate binding / sarcoplasmic reticulum / muscle contraction / calcium ion transmembrane transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / Z disc / transmembrane transporter binding / membrane => GO:0016020 / calmodulin binding / negative regulation of DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Yang, Z. / Panwar, P. / Van Petegem, F. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Structures of the junctophilin/voltage-gated calcium channel interface reveal hot spot for cardiomyopathy mutations. Authors: Yang, Z.F. / Panwar, P. / McFarlane, C.R. / Tuinte, W.E. / Campiglio, M. / Van Petegem, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rxq.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rxq.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rxq_validation.pdf.gz | 461.3 KB | Display | wwPDB validaton report |
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Full document | 7rxq_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 7rxq_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7rxq_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/7rxq ftp://data.pdbj.org/pub/pdb/validation_reports/rx/7rxq | HTTPS FTP |
-Related structure data
Related structure data | 7rw4SC 7rxeC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 36122.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JPH2, JP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BR39 | ||||
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#2: Protein/peptide | Mass: 1883.094 Da / Num. of mol.: 1 Fragment: EERIFRRTGGLFGQVD correspond to UNP residues 1594-1609 Source method: obtained synthetically / Source: (synth.) Oryctolagus cuniculus (rabbit) / References: UniProt: P07293 | ||||
#3: Chemical | ChemComp-EOH / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350, potassium sulphate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.03→44.34 Å / Num. obs: 19608 / % possible obs: 97.1 % / Redundancy: 3.18 % / Biso Wilson estimate: 30.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RW4 Resolution: 2.03→38.07 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.75 Å2 / Biso mean: 44.0478 Å2 / Biso min: 13.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.03→38.07 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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