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Yorodumi- PDB-6wud: Human Calcium and Integrin Binding Protein 3 Bound to TMC1 Residu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wud | ||||||
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Title | Human Calcium and Integrin Binding Protein 3 Bound to TMC1 Residues 303-347 | ||||||
Components |
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Keywords | METAL BINDING/TRANSPORT PROTEIN / EF-hand / Mechanotransduction / hearing / METAL BINDING PROTEIN / METAL BINDING-TRANSPORT PROTEIN complex | ||||||
Function / homology | Function and homology information vestibular reflex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / regulation of calcium ion transmembrane transport / plasma membrane => GO:0005886 / voltage-gated calcium channel activity / calcium ion homeostasis / calcium ion transmembrane transport / external side of plasma membrane ...vestibular reflex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / regulation of calcium ion transmembrane transport / plasma membrane => GO:0005886 / voltage-gated calcium channel activity / calcium ion homeostasis / calcium ion transmembrane transport / external side of plasma membrane / calcium ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Shapiro, L. / Dionne, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Neuron / Year: 2021 Title: CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells. Authors: Liang, X. / Qiu, X. / Dionne, G. / Cunningham, C.L. / Pucak, M.L. / Peng, G. / Kim, Y.H. / Lauer, A. / Shapiro, L. / Muller, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wud.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wud.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 6wud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wud_validation.pdf.gz | 419.4 KB | Display | wwPDB validaton report |
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Full document | 6wud_full_validation.pdf.gz | 419.5 KB | Display | |
Data in XML | 6wud_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 6wud_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/6wud ftp://data.pdbj.org/pub/pdb/validation_reports/wu/6wud | HTTPS FTP |
-Related structure data
Related structure data | 6wu5C 6wu7SC 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: 22309.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CIB3, KIP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96Q77 | ||||
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#2: Protein | Mass: 6281.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmc1, Bth, dn / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R4P5 | ||||
#3: Chemical | #4: 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: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% PEG 3350 0.2M Magnesium Chloride |
-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: 1.77 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 1.838→87.17 Å / Num. obs: 23155 / % possible obs: 90.83 % / Redundancy: 17.8 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.93 |
Reflection shell | Resolution: 1.838→1.904 Å / Num. unique obs: 1806 / CC1/2: 0.864 / % possible all: 72.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WU7 Resolution: 1.84→87.17 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7705 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 34.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→87.17 Å
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Refine LS restraints |
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LS refinement shell |
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