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Yorodumi- PDB-5ly3: P. calidifontis crenactin in complex with arcadin-2 C-terminal peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ly3 | ||||||
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Title | P. calidifontis crenactin in complex with arcadin-2 C-terminal peptide | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / actin / bacterial cytoskeleton | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrobaculum calidifontis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Izore, T. / Lowe, J. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Crenactin forms actin-like double helical filaments regulated by arcadin-2. Authors: Thierry Izoré / Danguole Kureisaite-Ciziene / Stephen H McLaughlin / Jan Löwe / Abstract: The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of ...The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of crenactin and actin are similar, although their filament architectures were suggested to be different. Here we report that crenactin forms double helical filaments that show exceptional similarity to eukaryotic F-actin. With cryo-electron microscopy and helical reconstruction we solved the structure of the crenactin filament to 3.8 Å resolution. When forming double filaments, the 'hydrophobic plug' loop in crenactin rearranges. Arcadin-2, also encoded by the arcade gene cluster, binds tightly with its C-terminus to the hydrophobic groove of crenactin. Binding is reminiscent of eukaryotic actin modulators such as cofilin and thymosin β4 and arcadin-2 is a depolymeriser of crenactin filaments. Our work further supports the theory of shared ancestry of Eukaryotes and Crenarchaea. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ly3.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ly3.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ly3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ly3_validation.pdf.gz | 761.9 KB | Display | wwPDB validaton report |
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Full document | 5ly3_full_validation.pdf.gz | 762.7 KB | Display | |
Data in XML | 5ly3_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5ly3_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/5ly3 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/5ly3 | HTTPS FTP |
-Related structure data
Related structure data | 4117C 5ly5C 5mw1C 4cj7S S: Starting model for refinement C: citing same article (ref.) |
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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: 48425.484 Da / Num. of mol.: 1 / Fragment: UNP residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Gene: Pcal_1635 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MWN5 |
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#2: Protein/peptide | Mass: 1846.140 Da / Num. of mol.: 1 / Fragment: UNP residues 188-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548 / VA1 / Gene: Pcal_1636 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MWN6 |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.31 M sodium acetate, 12.8 % (w/v) PEG 4000, 0.1 M sodium acetate, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 58765 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.897 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CJ7 Resolution: 1.6→45.948 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→45.948 Å
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Refine LS restraints |
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LS refinement shell |
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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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