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Yorodumi- PDB-8bnq: Crystal structure of the FnIII-tandem A84-A86 from the A-band of titin -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bnq | ||||||||||||
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Title | Crystal structure of the FnIII-tandem A84-A86 from the A-band of titin | ||||||||||||
Components | Titin | ||||||||||||
Keywords | STRUCTURAL PROTEIN / titin / muscle / A-band | ||||||||||||
Function / homology | Function and homology information sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / M band / I band / cardiac muscle cell development / regulation of protein kinase activity / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / cardiac muscle contraction / protein kinase A signaling / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Zacharchenko, T. / Fleming, J.R. / Mayans, O. | ||||||||||||
Funding support | United Kingdom, France, 3items
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Citation | Journal: J.Muscle Res.Cell.Motil. / Year: 2023 Title: Molecular insights into titin's A-band. Authors: Fleming, J.R. / Muller, I. / Zacharchenko, T. / Diederichs, K. / Mayans, O. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bnq.cif.gz | 263.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bnq.ent.gz | 203.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bnq_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 8bnq_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 8bnq_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 8bnq_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/8bnq ftp://data.pdbj.org/pub/pdb/validation_reports/bn/8bnq | HTTPS FTP |
-Related structure data
Related structure data | 2nziS S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33543.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase #2: Chemical | #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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 5% [v/v] polyethylene glycol 400 and 40% [v/v] 2-methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9725 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9725 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.5 Å / Num. obs: 27975 / % possible obs: 97.95 % / Redundancy: 3.6 % / Biso Wilson estimate: 45.69 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.121 / Net I/σ(I): 9.27 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2819 / CC1/2: 0.492 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NZI Resolution: 2.3→29.5 Å / SU ML: 0.3396 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.6361 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: 63.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.5 Å
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Refine LS restraints |
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LS refinement shell |
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