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Yorodumi- PDB-6zrn: Crystal structure of the RLIP76 Ral binding domain mutant (E427S/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zrn | ||||||
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Title | Crystal structure of the RLIP76 Ral binding domain mutant (E427S/L429M/Q433L/K440R) in complex with RalB-GMPPNP | ||||||
Components |
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Keywords | PROTEIN BINDING / RalB / RLIP76 / Ral binding domain / coiled-coil / small GTPase / G protein | ||||||
Function / homology | Function and homology information regulation of exocyst localization / doxorubicin transport / regulation of exocyst assembly / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / positive regulation of autophagosome assembly / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / regulation of Cdc42 protein signal transduction ...regulation of exocyst localization / doxorubicin transport / regulation of exocyst assembly / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / positive regulation of autophagosome assembly / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction / positive regulation of epidermal growth factor receptor signaling pathway / small GTPase-mediated signal transduction / positive regulation of mitochondrial fission / regulation of GTPase activity / cellular response to exogenous dsRNA / xenobiotic transmembrane transporter activity / CDC42 GTPase cycle / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / p38MAPK events / RAC1 GTPase cycle / cellular response to starvation / GTPase activator activity / small monomeric GTPase / G protein activity / positive regulation of GTPase activity / negative regulation of protein binding / positive regulation of protein serine/threonine kinase activity / receptor internalization / transmembrane transport / small GTPase binding / spindle pole / endocytosis / GDP binding / chemotaxis / positive regulation of protein binding / ATPase binding / midbody / Ras protein signal transduction / nuclear body / positive regulation of protein phosphorylation / cell division / GTPase activity / ubiquitin protein ligase binding / GTP binding / apoptotic process / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.482 Å | ||||||
Authors | Hurd, C. / Brear, P. / Revell, J. / Ross, S. / Mott, H. / Owen, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPases. Authors: Hurd, C.A. / Brear, P. / Revell, J. / Ross, S. / Mott, H.R. / Owen, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zrn.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zrn.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 6zrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zrn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6zrn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6zrn_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 6zrn_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/6zrn ftp://data.pdbj.org/pub/pdb/validation_reports/zr/6zrn | HTTPS FTP |
-Related structure data
Related structure data | 6zqtC 2kwiS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 20998.691 Da / Num. of mol.: 2 / Mutation: Q72L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RALB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P11234 #2: Protein | Mass: 6856.937 Da / Num. of mol.: 2 / Mutation: C411S, E427S, L429M, Q433L, K440R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RALBP1, RLIP1, RLIP76 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q15311 |
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-Non-polymers , 4 types, 250 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine 9.0 pH, 30% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→65.77 Å / Num. obs: 78582 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.069 / Rrim(I) all: 0.264 / Net I/σ(I): 8 / Num. measured all: 1159648 / Scaling rejects: 4407 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2KWI Resolution: 1.482→50.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.68 / 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: 85.41 Å2 / Biso mean: 30.8218 Å2 / Biso min: 12.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.482→50.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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