+Open data
-Basic information
Entry | Database: PDB / ID: 5vnz | ||||||
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Title | Structure of a TRAF6-Ubc13~Ub complex | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information PIP3 activates AKT signaling / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / Downstream TCR signaling / : / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / : / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 ...PIP3 activates AKT signaling / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / Downstream TCR signaling / : / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / : / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / : / : / : / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / : / : / Regulation of NF-kappa B signaling / MyD88 cascade initiated on plasma membrane / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Ub-specific processing proteases / : / UBC13-MMS2 complex / tumor necrosis factor receptor superfamily binding / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / tumor necrosis factor receptor binding / hypothalamus gonadotrophin-releasing hormone neuron development / postreplication repair / regulation of canonical NF-kappaB signal transduction / female meiosis I / positive regulation of double-strand break repair / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / positive regulation of intracellular signal transduction / fat pad development / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / non-canonical NF-kappaB signal transduction / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / regulation of DNA repair / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / lipopolysaccharide-mediated signaling pathway / 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 / negative regulation of TORC1 signaling / 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 / tumor necrosis factor-mediated signaling pathway / 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 / positive regulation of DNA repair / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.41 Å | ||||||
Authors | Middleton, A.J. / Day, C.L. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1. Authors: Middleton, A.J. / Budhidarmo, R. / Das, A. / Zhu, J. / Foglizzo, M. / Mace, P.D. / Day, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vnz.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vnz.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/5vnz ftp://data.pdbj.org/pub/pdb/validation_reports/vn/5vnz | HTTPS FTP |
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-Related structure data
Related structure data | 5vo0C 3hctS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 13709.656 Da / Num. of mol.: 2 / Fragment: residues 50-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: traf6, si:dkey-56p7.3, zgc:63704 / Production host: Escherichia coli (E. coli) References: UniProt: Q6IWL4*PLUS, RING-type E3 ubiquitin transferase #2: Protein | Mass: 17566.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli) References: UniProt: P61088, E2 ubiquitin-conjugating enzyme #3: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 #4: Chemical | ChemComp-ZN / |
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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: 3.59 Å3/Da / Density % sol: 65.76 % |
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Crystal grow | Temperature: 289 K / Method: microbatch Details: 0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.41→107.45 Å / Num. obs: 16046 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 9.7 | |||||||||||||||||||||
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: 3HCT Resolution: 3.41→107.45 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / SU B: 34.845 / SU ML: 0.505 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.604 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 245.82 Å2 / Biso mean: 155.826 Å2 / Biso min: 106.28 Å2
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Refinement step | Cycle: final / Resolution: 3.41→107.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.408→3.496 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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