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Yorodumi- PDB-5hpk: System-wide modulation of HECT E3 ligases with selective ubiquiti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hpk | ||||||
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Title | System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1 | ||||||
Components |
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Keywords | LIGASE / HECT / E3 ligase / NEDD4L / ubiquitin / Ubv | ||||||
Function / homology | Function and homology information positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization ...positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / regulation of membrane depolarization / positive regulation of dendrite extension / ventricular cardiac muscle cell action potential / potassium channel inhibitor activity / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of monoatomic ion transmembrane transport / regulation of dendrite morphogenesis / protein monoubiquitination / Peptide chain elongation / Selenocysteine synthesis / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / potassium channel regulator activity / sodium channel regulator activity / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein K48-linked ubiquitination / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / monoatomic ion transmembrane transport / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / multivesicular body / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.431 Å | ||||||
Authors | Wu, K.-P. / Mukherjee, M. / Mercredi, P.Y. / Schulman, B.A. | ||||||
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 | 5hpk.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hpk.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hpk_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 5hpk_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 5hpk_validation.xml.gz | 19 KB | Display | |
Data in CIF | 5hpk_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/5hpk ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpk | HTTPS FTP |
-Related structure data
Related structure data | 5c7jC 5c7mC 5hplC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45251.492 Da / Num. of mol.: 1 / Fragment: HECT domain (UNP residues 594-975) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein | Mass: 10050.478 Da / Num. of mol.: 1 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(DE3) / References: UniProt: P62987*PLUS |
#3: 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: 4.45 Å3/Da / Density % sol: 72.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium cacodylate, NaCl, PEG 8000, 1-butanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.431→45.976 Å / Num. obs: 38009 / % possible obs: 99.79 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 17.36 |
Reflection shell | Resolution: 2.431→2.4919 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.56 / % possible all: 99.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ND7 Resolution: 2.431→35.663 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.431→35.663 Å
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Refine LS restraints |
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LS refinement shell |
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