+Open data
-Basic information
Entry | Database: PDB / ID: 8etd | ||||||
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Title | Crystal Structure of Schizosaccharomyces pombe Rho1 | ||||||
Components | GTP-binding protein rho1 | ||||||
Keywords | GENE REGULATION / GTPase / Rho / GDP / Evolution | ||||||
Function / homology | Function and homology information positive regulation of (1->3)-beta-D-glucan biosynthetic process / regulation of fungal-type cell wall (1->3)-alpha-glucan biosynthetic process / positive regulation of primary cell septum biogenesis / regulation of establishment or maintenance of cell polarity regulating cell shape / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events / RHO GTPases activate PKNs / RHOD GTPase cycle / RHOF GTPase cycle ...positive regulation of (1->3)-beta-D-glucan biosynthetic process / regulation of fungal-type cell wall (1->3)-alpha-glucan biosynthetic process / positive regulation of primary cell septum biogenesis / regulation of establishment or maintenance of cell polarity regulating cell shape / PI3K/AKT activation / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events / RHO GTPases activate PKNs / RHOD GTPase cycle / RHOF GTPase cycle / RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / positive regulation of mitotic division septum assembly / cell cortex of growing cell tip / regulation of mitotic actomyosin contractile ring contraction / protein aggregate center / RHOA GTPase cycle / : / growing cell tip / regulation of fungal-type cell wall biogenesis / regulation of division septum assembly / Neutrophil degranulation / medial cortex / division septum / cortical cytoskeleton organization / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / regulation of endocytosis / signaling adaptor activity / actin filament organization / cell projection / regulation of actin cytoskeleton organization / regulation of cell shape / cell cortex / cytoplasmic vesicle / cytoskeleton / GTPase activity / GTP binding / protein kinase binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Huang, Q. / Xie, J. / Seetharaman, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Biology (Basel) / Year: 2022 Title: Crystal Structure of Schizosaccharomyces pombe Rho1 Reveals Its Evolutionary Relationship with Other Rho GTPases. Authors: Huang, Q. / Xie, J. / Seetharaman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8etd.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8etd.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 8etd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/8etd ftp://data.pdbj.org/pub/pdb/validation_reports/et/8etd | HTTPS FTP |
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-Related structure data
Related structure data | 5zvpS S: Starting model for refinement |
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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: 22555.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: rho1, SPAC1F7.04 / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q09914 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic tetrahydrate (pH 5.6), 1.9 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→50 Å / Num. obs: 12478 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.78→2.83 Å / Rmerge(I) obs: 0.82 / Num. unique obs: 617 / CC1/2: 0.514 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5zvp Resolution: 2.78→39.14 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.46 / 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: 95.02 Å2 / Biso mean: 23.7813 Å2 / Biso min: 3.79 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.78→39.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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