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Yorodumi- PDB-8q4j: The crystal structure of human chloride intracellular channel pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q4j | ||||||
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Title | The crystal structure of human chloride intracellular channel protein 5 delta 57-68 F34D mutant | ||||||
Components | Chloride intracellular channel protein 5Chloride channel | ||||||
Keywords | LIPID BINDING PROTEIN / CLIC5B / p64 / metamorphic protein | ||||||
Function / homology | Function and homology information stereocilium bundle / Sensory processing of sound by outer hair cells of the cochlea / response to stimulus / Sensory processing of sound by inner hair cells of the cochlea / chloride transport / chloride channel activity / chloride channel complex / visual perception / female pregnancy / sensory perception of sound ...stereocilium bundle / Sensory processing of sound by outer hair cells of the cochlea / response to stimulus / Sensory processing of sound by inner hair cells of the cochlea / chloride transport / chloride channel activity / chloride channel complex / visual perception / female pregnancy / sensory perception of sound / actin cytoskeleton / cell cortex / apical plasma membrane / centrosome / Golgi apparatus / mitochondrion / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Manori, B. / Giladi, M. / Haitin, Y. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Chloride intracellular channel (CLIC) proteins function as fusogens. Authors: Manori, B. / Vaknin, A. / Vankova, P. / Nitzan, A. / Zaidel-Bar, R. / Man, P. / Giladi, M. / Haitin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q4j.cif.gz | 178.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q4j.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 8q4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/8q4j ftp://data.pdbj.org/pub/pdb/validation_reports/q4/8q4j | HTTPS FTP |
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-Related structure data
Related structure data | 8q4iC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15151/ESRF-ES-1018419442 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25579.115 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZA1 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.26 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 7.0, 30% Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.886 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 2.505→45.478 Å / Num. obs: 22925 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rrim(I) all: 0.126 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.51→2.66 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3596 / CC1/2: 0.503 / Rrim(I) all: 1.975 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→42.42 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.74 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→42.42 Å
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Refine LS restraints |
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LS refinement shell |
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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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