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Yorodumi- PDB-6p0n: Crystal structure of GDP-bound human RalA in a covalent complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p0n | ||||||
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Title | Crystal structure of GDP-bound human RalA in a covalent complex with aryl sulfonyl fluoride compounds. | ||||||
Components | Ras-related protein Ral-A | ||||||
Keywords | signaling protein/inhibitor / Ral GTPase / RalA / covalent inhibitor / sulfonyl fluoride / SIGNALING PROTEIN / signaling protein-inhibitor complex | ||||||
Function / homology | Function and homology information membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / myosin binding / positive regulation of mitochondrial fission ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / myosin binding / positive regulation of mitochondrial fission / exocytosis / cleavage furrow / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / cytoplasmic vesicle membrane / Schaffer collateral - CA1 synapse / receptor internalization / chemotaxis / GDP binding / ATPase binding / Ras protein signal transduction / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / cell surface / signal transduction / mitochondrion / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Liu, D. / Ghozayel, M.K. / Xu, D. / Meroueh, S.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases. Authors: Bum-Erdene, K. / Liu, D. / Gonzalez-Gutierrez, G. / Ghozayel, M.K. / Xu, D. / Meroueh, S.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p0n.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p0n.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 6p0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p0n_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6p0n_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6p0n_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6p0n_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/6p0n ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p0n | HTTPS FTP |
-Related structure data
Related structure data | 6p0iC 6p0jC 6p0kC 6p0lC 6p0mC 6p0oC 1u8zS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 21303.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RALA, RAL / Production host: Escherichia coli (E. coli) / References: UniProt: P11233 |
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-Non-polymers , 5 types, 231 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NLS / | #5: Chemical | ChemComp-GDP / | #6: 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: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Calcium Acetate pH 5.5, 18-22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→55.31 Å / Num. obs: 23868 / % possible obs: 98.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.066 / Rrim(I) all: 0.179 / Rsym value: 0.166 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.63→1.7 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2773 / CC1/2: 0.621 / Rpim(I) all: 0.629 / Rrim(I) all: 1.689 / Rsym value: 1.567 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U8Z Resolution: 1.63→55.31 Å / SU ML: 0.1605 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9952
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→55.31 Å
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Refine LS restraints |
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LS refinement shell |
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