+Open data
-Basic information
Entry | Database: PDB / ID: 4xa6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the coiled-coil surrounding Skip 4 of MYH7 | ||||||
Components | Gp7-MYH7(1777-1855)-EB1 chimera protein | ||||||
Keywords | MOTOR PROTEIN / Myosin / coiled coil / skip residue / fusion / Gp7 / EB1 / MYH7 / Cardiac | ||||||
Function / homology | Function and homology information viral scaffold / protein localization to astral microtubule / regulation of slow-twitch skeletal muscle fiber contraction / cortical microtubule cytoskeleton / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / muscle myosin complex / muscle filament sliding ...viral scaffold / protein localization to astral microtubule / regulation of slow-twitch skeletal muscle fiber contraction / cortical microtubule cytoskeleton / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / muscle myosin complex / muscle filament sliding / cell projection membrane / transition between fast and slow fiber / regulation of the force of heart contraction / attachment of mitotic spindle microtubules to kinetochore / myosin filament / microtubule plus-end binding / non-motile cilium assembly / adult heart development / microtubule bundle formation / cardiac muscle hypertrophy in response to stress / myosin II complex / myosin complex / protein localization to centrosome / microtubule organizing center / ventricular cardiac muscle tissue morphogenesis / negative regulation of microtubule polymerization / sarcomere organization / microfilament motor activity / myofibril / virion assembly / mitotic spindle pole / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule polymerization / skeletal muscle contraction / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / striated muscle contraction / muscle contraction / cardiac muscle contraction / stress fiber / ATP metabolic process / 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 / regulation of heart rate / sarcomere / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / Z disc / 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 / cell migration / microtubule / calmodulin binding / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / DNA binding / RNA binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å | ||||||
Authors | Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinz, N.T. / Qiang, C. / Leinwand, L.A. / Rayment, I. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Authors: Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinze, N.T. / Cui, Q. / Leinwand, L.A. / Rayment, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xa6.cif.gz | 246.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xa6.ent.gz | 204.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xa6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xa6_validation.pdf.gz | 476.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xa6_full_validation.pdf.gz | 492.5 KB | Display | |
Data in XML | 4xa6_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4xa6_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xa6 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xa6 | HTTPS FTP |
-Related structure data
Related structure data | 4xa1C 4xa3C 4xa4C 1no4S 1yibS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21221.461 Da / Num. of mol.: 4 Fragment: UNP P13848 residues 2-50,UNP P02564 residues 1777-1855,UNP Q15691 residues 209-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human) Plasmid: pET28 / Gene: MYH7, MYHCB, MAPRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P13848, UniProt: P12883, UniProt: Q15691 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 67 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 18% (w/v) polyethylene glycol 2000 methyl ether, 100 mM piperazine-N,N-bis(2-ethanesulfonic acid) (PIPES) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 9, 2014 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 15120 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.08 / Net I/av σ(I): 10.1 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NO4, 1YIB Resolution: 3.42→43.887 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.27 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.42→43.887 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|