+Open data
-Basic information
Entry | Database: PDB / ID: 2fxo | ||||||
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Title | Structure of the human beta-myosin S2 fragment | ||||||
Components | Myosin heavy chain, cardiac muscle beta isoform | ||||||
Keywords | CONTRACTILE PROTEIN / COILED COIL (DIMERIC / PARALLEL) / FAMILIAL HYPERTROPHIC CARDIOMYOPATHY / FHC-ASSOCIATED MUTANT E924K / THICK FILAMENT | ||||||
Function / homology | Function and homology information regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / muscle contraction / cardiac muscle contraction / stress fiber / ATP metabolic process / regulation of heart rate / sarcomere / Z disc / actin filament binding / calmodulin binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD WITH SEMI-BRUTE- FORCE MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Blankenfeldt, W. / Thoma, N.H. / Wray, J.S. / Gautel, M. / Schlichting, I. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2006 Title: Crystal structures of human cardiac beta-myosin II S2-Delta provide insight into the functional role of the S2 subfragment. Authors: Wulf Blankenfeldt / Nicolas H Thomä / John S Wray / Mathias Gautel / Ilme Schlichting / Abstract: Myosin II is the major component of the muscle thick filament. It consists of two N-terminal S1 subfragments ("heads") connected to a long dimeric coiled-coil rod. The rod is in itself twofold ...Myosin II is the major component of the muscle thick filament. It consists of two N-terminal S1 subfragments ("heads") connected to a long dimeric coiled-coil rod. The rod is in itself twofold symmetric, but in the filament, the two heads point away from the filament surface and are therefore not equivalent. This breaking of symmetry requires the initial section of the rod, subfragment 2 (S2), to be relatively flexible. S2 is an important functional element, involved in various mechanisms by which the activity of smooth and striated muscle is regulated. We have determined crystal structures of the 126 N-terminal residues of S2 from human cardiac beta-myosin II (S2-Delta), of both WT and the disease-associated E924K mutant. S2-Delta is a straight parallel dimeric coiled coil, but the N terminus of one chain is disordered in WT-S2-Delta due to crystal contacts, indicative of unstable local structure. Bulky noncanonical side chains pack into a/d positions of S2-Delta's N terminus, leading to defined local asymmetry and axial stagger, which could induce nonequivalence of the S1 subfragments. Additionally, S2 possesses a conserved charge distribution with three prominent rings of negative potential within S2-Delta, the first of which may provide a binding interface for the "blocked head" of smooth muscle myosin in the OFF state. The observation that many disease-associated mutations affect the second negatively charged ring further suggests that charge interactions play an important role in regulation of cardiac muscle activity through myosin-binding protein C. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Mutations in Beta-Myosin S2 that Cause Familial Hypertrophic Cardiomyopathy (Fhc) Abolish the Interaction with the Regulatory Domain of Myosin-Binding Protein-C Authors: Gruen, M. / Gautel, M. #2: Journal: Nature / Year: 2003 Title: Visualization of an Unstable Coiled Coil from the Scallop Myosin Rod Authors: Li, Y. / Brown, J.H. / Reshetnikova, L. / Blazsek, A. / Farkas, L. / Nyitray, L. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fxo.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fxo.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fxo_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 2fxo_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 2fxo_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2fxo_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/2fxo ftp://data.pdbj.org/pub/pdb/validation_reports/fx/2fxo | HTTPS FTP |
-Related structure data
Related structure data | 2fxmC 1xnm 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15106.145 Da / Num. of mol.: 4 / Fragment: DELTA-S2 FRAGMENT (838-963) / Mutation: E924K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: HEART MUSCLE / Gene: HSBMHC / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12883 |
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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: 2.6 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, SODIUM ACETATE, TRIS-HCL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 16, 2001 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 20190 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.08 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.388 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD WITH SEMI-BRUTE- FORCE MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XNM 1xnm Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.647 / SU ML: 0.458 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.891 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Hydrogens have been added in the riding positions. Target sigma values for restrained B-factor refinement have been relaxed to 10 A*A to reflect the special shape of the molecule. Atoms that ...Details: Hydrogens have been added in the riding positions. Target sigma values for restrained B-factor refinement have been relaxed to 10 A*A to reflect the special shape of the molecule. Atoms that could not be located have been assigned a temperature factor of 500 A*A and occupancy value of 0 for better discernability.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20 /
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Refinement TLS params. | T33: 0.1116 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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