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Yorodumi- PDB-3mtu: Structure of the Tropomyosin Overlap Complex from Chicken Smooth ... -
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-Basic information
Entry | Database: PDB / ID: 3mtu | ||||||
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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 viral scaffold / Smooth Muscle Contraction / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / Striated Muscle Contraction / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore ...viral scaffold / Smooth Muscle Contraction / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / Striated Muscle Contraction / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / virion assembly / mitotic spindle pole / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule polymerization / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cardiac muscle contraction / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / cytoskeletal protein binding / AURKA Activation by TPX2 / ciliary basal body / actin filament organization / actin filament / RHO GTPases Activate Formins / actin filament binding / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / protein localization / actin cytoskeleton / cell migration / microtubule / cadherin binding / protein heterodimerization activity / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / protein homodimerization activity / DNA binding / RNA binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Homo sapiens (human) Bacillus phage phi29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 | 3mtu.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mtu.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mtu_validation.pdf.gz | 496.3 KB | Display | wwPDB validaton report |
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Full document | 3mtu_full_validation.pdf.gz | 506 KB | Display | |
Data in XML | 3mtu_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 3mtu_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/3mtu ftp://data.pdbj.org/pub/pdb/validation_reports/mt/3mtu | HTTPS FTP |
-Related structure data
-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 on special symmetry positions |
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-Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 8713.371 Da / Num. of mol.: 4 Fragment: Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and residues 215-257 of human EB1 protein,Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and ...Fragment: Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and residues 215-257 of human EB1 protein,Fusion protein of residues 1-29 of chicken smooth muscle tropomyosin and residues 215-257 of human EB1 protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human) Gene: TPM1, MAPRE1 / Plasmid: pET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P04268, UniProt: Q15691 #2: Protein | Mass: 8956.418 Da / Num. of mol.: 2 Fragment: Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues 256-284 of chicken smooth muscle tropomyosin,Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues ...Fragment: Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues 256-284 of chicken smooth muscle tropomyosin,Fusion protein of residues 2-45 of phage phi29 Gp7 protein and residues 256-284 of chicken smooth muscle tropomyosin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Gallus gallus (chicken) Plasmid: pET31B / Gene: TPM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P13848, UniProt: P04268 |
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-Non-polymers , 4 types, 365 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-EOH / #6: 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: 2.62 Å3/Da / Density % sol: 53.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16% MePEG 5000, 100 mM MES, pH 6.0, 140 mM CaCl2, 2% methanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
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Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 15, 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: 2.1→30 Å / Num. all: 33163 / Num. obs: 33097 / % possible obs: 99.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 3.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→29.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.393 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.178 / 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: 1.25 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.193 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.098→2.152 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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