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Yorodumi- PDB-3mud: Structure of the Tropomyosin Overlap Complex from Chicken Smooth ... -
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-Basic information
Entry | Database: PDB / ID: 3mud | ||||||
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Title | Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / tropomysoin / overlap complex / coiled-coils | ||||||
Function / homology | Function and homology information positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Smooth Muscle Contraction / FHA domain binding / protein localization to astral microtubule / cortical microtubule cytoskeleton / positive regulation of ligase activity / mitotic spindle astral microtubule end / DNA ligase IV complex / DNA ligation involved in DNA repair ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Smooth Muscle Contraction / FHA domain binding / protein localization to astral microtubule / cortical microtubule cytoskeleton / positive regulation of ligase activity / mitotic spindle astral microtubule end / DNA ligase IV complex / DNA ligation involved in DNA repair / protein localization to microtubule / bleb / Striated Muscle Contraction / microtubule plus-end / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / cell projection membrane / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / ruffle organization / non-motile cilium assembly / microtubule bundle formation / Striated Muscle Contraction / positive regulation of ATP-dependent activity / protein localization to centrosome / regulation of heart contraction / structural constituent of muscle / sarcomere organization / microtubule organizing center / negative regulation of microtubule polymerization / ventricular cardiac muscle tissue morphogenesis / cellular response to lithium ion / 2-LTR circle formation / mitotic spindle pole / microtubule polymerization / negative regulation of vascular associated smooth muscle cell proliferation / establishment of mitotic spindle orientation / response to X-ray / positive regulation of cell adhesion / Smooth Muscle Contraction / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / stress fiber / Mitotic Prometaphase / cytoskeleton organization / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of stress fiber assembly / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cytoskeletal protein binding / sarcomere / AURKA Activation by TPX2 / negative regulation of cell migration / ciliary basal body / actin filament organization / actin filament / RHO GTPases Activate Formins / Nonhomologous End-Joining (NHEJ) / wound healing / protein localization / structural constituent of cytoskeleton / ruffle membrane / cellular response to reactive oxygen species / double-strand break repair via nonhomologous end joining / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / double-strand break repair / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / cell migration / actin cytoskeleton / site of double-strand break / actin binding / regulation of cell shape / microtubule / molecular adaptor activity / cytoskeleton / cadherin binding / protein heterodimerization activity / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Klenchin, V.A. / Frye, J. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structure of the tropomyosin overlap complex from chicken smooth muscle: insight into the diversity of N-terminal recognition . Authors: Frye, J. / Klenchin, V.A. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mud.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mud.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/3mud ftp://data.pdbj.org/pub/pdb/validation_reports/mu/3mud | HTTPS FTP |
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-Related structure data
Related structure data | 3mtuC 1fu1S 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: 19743.168 Da / Num. of mol.: 2 / Mutation: I134T, L249N,I134T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Gallus gallus (chicken) Gene: XRCC4, TPM1 / Plasmid: pET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: Q13426, UniProt: P04268 #2: Protein | Mass: 8572.687 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPM1, C15orf13, TMSA, MAPRE1 / Plasmid: pET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P09493, UniProt: Q15691 #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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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: 3.35 Å3/Da / Density % sol: 63.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% MePEG 2000, 100 mM Bis-Tris, 120 mM MgSO4 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Aug 6, 2009 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 39926 / Num. obs: 39647 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 49.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 5.8 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FU1 Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.66 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.235 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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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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