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Yorodumi- PDB-7whg: Lokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin -
+Open data
-Basic information
Entry | Database: PDB / ID: 7whg | |||||||||||||||
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Title | Lokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin | |||||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Asgard / gelsolin / actin / filament | |||||||||||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) Candidatus Lokiarchaeota archaeon (archaea) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | |||||||||||||||
Authors | Robinson, R.C. / Akil, C. | |||||||||||||||
Funding support | 4items
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Citation | Journal: Commun Biol / Year: 2022 Title: Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis Authors: Akil, C. / Tran, L.T. / Orhant-Prioux, M. / Baskaran, Y. / Senju, Y. / Takeda, S. / Chotchuang, P. / Muengsaen, D. / Schulte, A. / Manser, E. / Blanchoin, L. / Robinson, R.C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7whg.cif.gz | 408.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7whg.ent.gz | 318.1 KB | Display | PDB format |
PDBx/mmJSON format | 7whg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/7whg ftp://data.pdbj.org/pub/pdb/validation_reports/wh/7whg | HTTPS FTP |
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-Related structure data
Related structure data | 7whfC 3hbtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42109.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | | Mass: 37544.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Lokiarchaeota archaeon (archaea) Production host: Escherichia coli (E. coli) #3: Chemical | #4: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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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: 52.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.4 mM Loki2DGel 0.4 mM rabbit actin 0.1 M Tris-HCl, pH 7.0 0.2 M magnesium chloride hexahydrate 10% w/v polyethylene glycol 8000 1 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: May 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→20 Å / Num. obs: 17387 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.887 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.077 / Rrim(I) all: 0.183 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.25→3.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1504 / CC1/2: 0.523 / Rpim(I) all: 0.578 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HBT Resolution: 3.25→20 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 68.14 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.46 Å /
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