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- PDB-3dtp: Tarantula heavy meromyosin obtained by flexible docking to Tarant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dtp | ||||||||||||||||||||||||||||||
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Title | Tarantula heavy meromyosin obtained by flexible docking to Tarantula muscle thick filament Cryo-EM 3D-MAP | ||||||||||||||||||||||||||||||
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Function / homology | Kinesin motor domain superfamily / Myosin S1 fragment, N-terminal / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Specimen source | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||||||||||||||
![]() | Alamo, L. / Wriggers, W. / Pinto, A. / Bartoli, F. / Salazar, L. / Zhao, F.Q. / Craig, R. / Padron, R. | ||||||||||||||||||||||||||||||
![]() | Journal: Cell / Year: 1999 Title: Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head. ![]() | ||||||||||||||||||||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Date | Deposition: Jul 15, 2008 / Release: Oct 7, 2008
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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-Related structure data
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Assembly
Deposited unit | ![]()
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1 | ![]()
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3 | ![]()
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Helical symmetry | Circular symmetry: 4 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 36 / Rise per n subunits: 145 / Rotation per n subunits: 3 |
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Components
#1: Protein/peptide | Mass: 111851.070 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-972) / Source: (gene. exp.) Gallus gallus, Homo sapiens / Plasmid name: PVL1392, PET / Cell line (production host): SF9 Production host: Spodoptera frugiperda, Escherichia coli BL21 Strain (production host): BL21 / References: UniProt: P10587, UniProt: P12883 | ||||
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#2: Protein/peptide | Mass: 112051.328 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-974) / Source: (gene. exp.) Gallus gallus, Homo sapiens / Plasmid name: PVL1392, PET / Cell line (production host): SF9 Production host: Spodoptera frugiperda, Escherichia coli BL21 Strain (production host): BL21 / References: UniProt: P10587, UniProt: P12883 | ||||
#3: Protein/peptide | Mass: 16873.025 Da / Num. of mol.: 2 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Protein/peptide | Mass: 21709.250 Da / Num. of mol.: 2 / Source: (natural) ![]() ![]() Sequence details | THE CONFLICT LISTED FOR CHAINS A AND B, RESIDUE 2 ARE CONSISTENT WITH PDB ENTRY 1BR1 AND 1I84. THE ...THE CONFLICT LISTED FOR CHAINS A AND B, RESIDUE 2 ARE CONSISTENT | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / Reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Myosin thick filaments from Tarantula striated muscle / Type: COMPLEX Details: Polymer of a multiple myosin assembled over a paramyosin core. MODEL BUILDING: the atomic model consists of two s1 heads and a segment of s2. each heavy meromyosin consists of a chimera built by chicken smooth muscle heavy chain (1i84) for s1 plus human cardiac muscle (2fxm) for s2 (chains a,b) and two light chains, the chicken smooth muscle (1i84) for elc (chains c,d) and a homology model based on 1br1 of the tarantula skeletal muscle rlc sequence (chains e,f), this model was flexible fitted to a tarantula 3d map (emd-1535) |
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Buffer solution | Name: 100mM NaCl, 3mM MgCl2, 1mM EGTA, 5mM PIPES, 5mM NaH2PO4, 1mM NaN3 Details: 100mM NaCl, 3mM MgCl2, 1mM EGTA, 5mM PIPES, 5mM NaH2PO4, 1mM NaN3 pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Details: Holey carbon grids, 400 mesh |
Vitrification![]() | Details: Plunging in a liquid ethane. Blotting was performed from one side of the grid till a thin sample film on it using Whatman No 42 filter paper, then the grid was immediately plunged under gravity into liquid ethane cooled by liquid nitrogen. Grids were stored under liquid nitrogen. |
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Electron microscopy imaging
Microscopy | Microscope model: FEI/PHILIPS CM120T / Date: Sep 19, 2001 Details: Holey carbon grids Cryo preserved in Liquid ethane were observed in a Philips CM120 electron microscope under low dose conditions. Only filaments on thin carbon over holes were photographed |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 120 / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Temperature: 88 |
Image scans | Number digital images: 465 |
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Processing
EM software |
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CTF correction![]() | Details: no corrected | ||||||||||||
3D reconstruction | Method: Single particle reconstruction with a modification of the IHRSR method Resolution: 20 / Number of particles: 15504 / Nominal pixel size: 2.48 / Actual pixel size: 2.48 / Magnification calibration: Tropomyosin paracrystal Details: three-dimensional single particle reconstruction was carried out by a modification of the ihrsr method, using spider. low-dose electron micrographs of 1008 frozen-hydrated thick filaments halves were digitized at 0.248 nm per pixel using a nikon super coolscan 8000 ed scanner. filaments were aligned with the bare zone at the top, to ensure correct polarity in subsequent steps. a total of 15,504 segments, each 62 nm long, with an overlap of 55.8 nm, and containing aprox. 40,000 unique pairs of interacting myosin heads went into the reconstruction. as an initial reference model we used the tarantula negatively stained 3d-map, which was axially rotated, axially shifted and also out of plane tilted up to plus-minus12deg. for projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus 12 deg. every 2 deg., 45 reference rotated projections (0-90 deg., every 2 deg. rotation angle), and 7 image axial shifts of 2.2 nm. the resulting 3d-map combines about 10,700 out of 15,504 filament segments, a yield of 69 percent of included segments. Symmetry type: HELICAL | ||||||||||||
Atomic model building | Details: METHOD--Flexible Fitting REFINEMENT PROTOCOL--Custom skeleton of 31 positional markers Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Constrained Molecular Dynamics | ||||||||||||
Atomic model building |
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Number of atoms included #LAST | Protein: 20580 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 20580 |