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Yorodumi- PDB-5hpl: System-wide modulation of HECT E3 ligases with selective ubiquiti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hpl | ||||||
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Title | System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5 and UbV R5.4 | ||||||
Components |
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Keywords | LIGASE / HECT E3 / Rsp5 / Ubiquitin / Ubv | ||||||
Function / homology | Function and homology information regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / RHOQ GTPase cycle / RHOU GTPase cycle ...regulation of dolichol biosynthetic process / RSP5-BUL ubiquitin ligase complex / regulation of ribosomal large subunit export from nucleus / regulation of tRNA processing / regulation of tRNA export from nucleus / regulation of ubiquinone biosynthetic process / regulation of phosphate metabolic process / regulation of ergosterol biosynthetic process / RHOQ GTPase cycle / RHOU GTPase cycle / positive regulation of ubiquitin-dependent endocytosis / regulation of multivesicular body size / cellular response to L-arginine / ubiquitin-dependent endocytosis / ribophagy / mitochondria-associated ubiquitin-dependent protein catabolic process / free ubiquitin chain polymerization / regulation of mRNA export from nucleus / regulation of rRNA processing / cellular bud tip / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / actin cortical patch / positive regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / nonfunctional rRNA decay / ubiquitin-ubiquitin ligase activity / poly(A)+ mRNA export from nucleus / Regulation of PTEN stability and activity / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of endocytosis / Peptide chain elongation / Selenocysteine synthesis / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / phosphatidylinositol binding / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / cellular response to amino acid stimulus / Downregulation of TGF-beta receptor signaling / EGFR downregulation Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Wu, K.-P. / Kamadurai, H.B. / Schulman, B.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol.Cell / Year: 2016 Title: System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / ...Authors: Zhang, W. / Wu, K.P. / Sartori, M.A. / Kamadurai, H.B. / Ordureau, A. / Jiang, C. / Mercredi, P.Y. / Murchie, R. / Hu, J. / Persaud, A. / Mukherjee, M. / Li, N. / Doye, A. / Walker, J.R. / Sheng, Y. / Hao, Z. / Li, Y. / Brown, K.R. / Lemichez, E. / Chen, J. / Tong, Y. / Harper, J.W. / Moffat, J. / Rotin, D. / Schulman, B.A. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hpl.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hpl.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hpl_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 5hpl_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 5hpl_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 5hpl_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/5hpl ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpl | HTTPS FTP |
-Related structure data
Related structure data | 5c7jC 5c7mC 5hpkC 5hpsC 5hptC 1nd7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44864.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P39940 #2: Protein | Mass: 9876.315 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSF-duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P62987*PLUS #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: 2.46 Å3/Da / Density % sol: 50.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Bis-Tris 0.1M, pH 5.5 ammonium acetate 0.2 M, PEG 3350 14% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→80.482 Å / Num. obs: 45796 / % possible obs: 98.17 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.72 |
Reflection shell | Resolution: 2.31→2.393 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.41 / % possible all: 98.58 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ND7 Resolution: 2.31→80.482 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.21 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→80.482 Å
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Refine LS restraints |
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LS refinement shell |
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