+Open data
-Basic information
Entry | Database: PDB / ID: 5tgc | ||||||
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Title | Structure of the hetero-trimer of Rtt102-Arp7/9 bound to ATP | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Chromatin remodeling complexes / Actin-related protein / ATP-binding site / Nuclear actin | ||||||
Function / homology | Function and homology information RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / NuA4 histone acetyltransferase complex / chromosome segregation ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / NuA4 histone acetyltransferase complex / chromosome segregation / transcription elongation by RNA polymerase II / chromatin organization / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / structural molecule activity / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.245 Å | ||||||
Authors | Turegun, B. / Dominguez, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2018 Title: Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Authors: Turegun, B. / Baker, R.W. / Leschziner, A.E. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tgc.cif.gz | 993.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tgc.ent.gz | 842.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tgc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5tgc_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5tgc_validation.xml.gz | 57.9 KB | Display | |
Data in CIF | 5tgc_validation.cif.gz | 78.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/5tgc ftp://data.pdbj.org/pub/pdb/validation_reports/tg/5tgc | HTTPS FTP |
-Related structure data
Related structure data | 4i6mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 55433.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ARP7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12406 #2: Protein | Mass: 53131.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ARP9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05123 #3: Protein | Mass: 17904.693 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RTT102 / Production host: Escherichia coli (E. coli) / References: UniProt: P53330 #4: Chemical | #5: Chemical | |
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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: 52.77 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / Details: 0.17M Ammonium Sulfate, 20% PEG 3350, 17 mM EDTA / PH range: 6 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Dec 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.245→39.366 Å / Num. obs: 40398 / % possible obs: 96.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Rsym value: 0.087 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.25→3.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.418 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I6M, chains A,B,D Resolution: 3.245→39.366 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 234.41 Å2 / Biso mean: 70.1963 Å2 / Biso min: 31.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.245→39.366 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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