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Open data
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Basic information
Entry | Database: PDB / ID: 2wp3 | ||||||
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Title | Crystal structure of the Titin M10-Obscurin like 1 Ig complex | ||||||
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![]() | TRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / SARCOMERE / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / KELCH REPEAT / CARDIOMYOPATHY / CALMODULIN-BINDING | ||||||
Function / homology | ![]() 3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cytoskeletal anchor activity ...3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cytoskeletal anchor activity / 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 / positive regulation of dendrite morphogenesis / structural constituent of muscle / regulation of mitotic nuclear division / sarcomere organization / Golgi organization / skeletal muscle thin filament assembly / striated muscle thin filament / intercalated disc / striated muscle contraction / cardiac muscle contraction / cytoskeleton organization / protein kinase A signaling / condensed nuclear chromosome / muscle contraction / positive regulation of protein secretion / Z disc / microtubule cytoskeleton organization / response to calcium ion / : / actin filament binding / Platelet degranulation / Neddylation / protein tyrosine kinase activity / protease binding / non-specific serine/threonine protein kinase / calmodulin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / calcium ion binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernigo, S. / Fuzukawa, A. / Gautel, M. / Steiner, R.A. | ||||||
![]() | ![]() Title: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex. Authors: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.1 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 455.2 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11125.619 Da / Num. of mol.: 1 / Fragment: IG1, RESIDUES 1-106 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 10981.231 Da / Num. of mol.: 1 / Fragment: M10, RESIDUES 34252-34350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Sequence details | INITIAL GSS ARE FROM THE EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN COMPLEX AT 13 MG/ML 2M AMM SULPHATE, 0.1 M BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 21, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9745 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→53.38 Å / Num. obs: 30142 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PREVIOUSLY SOLVED STRUCTURE FROM IN-HOUSE DATA Resolution: 1.48→33.19 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.202 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.578 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→33.19 Å
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