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Open data
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Basic information
Entry | Database: PDB / ID: 3jw0 | ||||||
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Title | E2~Ubiquitin-HECT | ||||||
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![]() | LIGASE/SIGNALING PROTEIN / Ubiquitin / HECT / E3 / Ubiquitin ligase / UbcH5B / NEDD4L / NEDD4-2 / Ligase / Ubl conjugation pathway / Isopeptide bond / Nucleus / Host-virus interaction / LIGASE-SIGNALING PROTEIN complex | ||||||
Function / homology | ![]() 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 ...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 / protein modification process => GO:0036211 / regulation of membrane repolarization / (E3-independent) E2 ubiquitin-conjugating enzyme / 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 / E2 ubiquitin-conjugating enzyme / regulation of dendrite morphogenesis / protein monoubiquitination / Peptide chain elongation / Selenocysteine synthesis / ubiquitin conjugating enzyme activity / 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 / potassium channel regulator activity / sodium channel regulator activity / Major pathway of rRNA processing in the nucleolus and cytosol / protein autoubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / protein K48-linked ubiquitination / ubiquitin ligase complex / Maturation of protein E / monoatomic ion transmembrane transport / 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 / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamadurai, H.B. / Schulman, B.A. | ||||||
![]() | ![]() Title: Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Authors: Kamadurai, H.B. / Souphron, J. / Scott, D.C. / Duda, D.M. / Miller, D.J. / Stringer, D. / Piper, R.C. / Schulman, B.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.2 KB | Display | ![]() |
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PDB format | ![]() | 198.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.3 KB | Display | ![]() |
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Full document | ![]() | 531.3 KB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 64.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | ACX / BDY |
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Components
#1: Protein | Mass: 16609.963 Da / Num. of mol.: 2 / Mutation: L3S, C85S, T98K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 45451.637 Da / Num. of mol.: 2 / Fragment: NEDD4L HECT DOMAIN (UNP 576-955) / Mutation: UBIQUITIN G76 ESTER-LINKED TO UBCH5B TO S85 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96PU5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #3: Protein | Mass: 8922.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 34028 / Observed criterion σ(F): 0 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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