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Yorodumi- PDB-4aow: Crystal structure of the human Rack1 protein at a resolution of 2... -
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-Basic information
Entry | Database: PDB / ID: 4aow | ||||||
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Title | Crystal structure of the human Rack1 protein at a resolution of 2.45 angstrom | ||||||
Components | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | ||||||
Keywords | RECEPTOR / WD-REPEAT / BETA-PROPELLER | ||||||
Function / homology | Function and homology information negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis ...negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / ion channel inhibitor activity / pigmentation / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / phagocytic cup / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / translation regulator activity / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / gastrulation / enzyme activator activity / rescue of stalled ribosome / SH2 domain binding / cyclin binding / positive regulation of GTPase activity / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of protein binding / cellular response to glucose stimulus / protein kinase C binding / Regulation of TNFR1 signaling / positive regulation of protein-containing complex assembly / negative regulation of cell growth / receptor tyrosine kinase binding / cellular response to growth factor stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of protein localization / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome binding / small ribosomal subunit / midbody / perikaryon / protein phosphatase binding / cytosolic small ribosomal subunit / molecular adaptor activity / cytoplasmic translation / negative regulation of translation / regulation of cell cycle / protein ubiquitination / positive regulation of cell migration / cadherin binding / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / negative regulation of gene expression / signaling receptor binding / neuronal cell body / dendrite / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Ruiz Carrillo, D. / Chandrasekaran, R. / Nilsson, M. / Cornvick, T. / Liew, C.W. / Tan, S.M. / Lescar, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of Human Rack1 Protein at a Resolution of 2.45 A. Authors: Ruiz Carrillo, D. / Chandrasekaran, R. / Nilsson, M. / Cornvik, T. / Liew, C.W. / Tan, S.M. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aow.cif.gz | 360.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aow.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 4aow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aow_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
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Full document | 4aow_full_validation.pdf.gz | 477.1 KB | Display | |
Data in XML | 4aow_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 4aow_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/4aow ftp://data.pdbj.org/pub/pdb/validation_reports/ao/4aow | HTTPS FTP |
-Related structure data
Related structure data | 3dm0S S: Starting model for refinement |
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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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 37805.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA T1R / References: UniProt: P63244 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.36 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.63 Å / Num. obs: 45262 / % possible obs: 98.8 % / Observed criterion σ(I): 2.5 / Redundancy: 9.3 % / Biso Wilson estimate: 50.28 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.45→2.59 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.5 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DM0 Resolution: 2.45→35.87 Å / Cor.coef. Fo:Fc: 0.9078 / Cor.coef. Fo:Fc free: 0.8901 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 45.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.327 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→35.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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