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- PDB-7bbd: Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In c... -
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Basic information
Entry | Database: PDB / ID: 7bbd | ||||||||||||
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Title | Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 | ||||||||||||
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![]() | LIGASE / E3 ubiquitin ligase / E2 conjugating enzyme / ubiquitin chain elongation | ||||||||||||
Function / homology | ![]() negative regulation of protein deubiquitination / error-free postreplication DNA repair / : / UBC13-MMS2 complex / regulation of viral entry into host cell / protein K27-linked ubiquitination / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination ...negative regulation of protein deubiquitination / error-free postreplication DNA repair / : / UBC13-MMS2 complex / regulation of viral entry into host cell / protein K27-linked ubiquitination / ubiquitin conjugating enzyme complex / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / hypothalamus gonadotrophin-releasing hormone neuron development / postreplication repair / stress granule disassembly / 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 / negative regulation of NF-kappaB transcription factor activity / seminiferous tubule development / male meiosis I / pyroptotic inflammatory response / response to type II interferon / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / autophagosome / proteasomal protein catabolic process / protein autoubiquitination / protein K48-linked ubiquitination / regulation of DNA repair / positive regulation of autophagy / positive regulation of cell cycle / 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) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / negative regulation of TORC1 signaling / 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 / positive regulation of DNA repair / 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 / negative regulation of innate immune response / 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 / 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 / neuron projection morphogenesis Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kiss, L. / Neuhaus, D. / James, L.C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination. Authors: Kiss, L. / Clift, D. / Renner, N. / Neuhaus, D. / James, L.C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.6 KB | Display | ![]() |
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PDB format | ![]() | 186.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bbfC ![]() 1j74S ![]() 1ubqS ![]() 6s53S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Polyubiquitin- ... , 2 types, 2 molecules BD
#1: Protein | Mass: 18379.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: J3QS39, UniProt: P19474, UniProt: P0CG47*PLUS, RING-type E3 ubiquitin transferase |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 / Mutation: G75A, G76A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Ubiquitin-conjugating enzyme E2 ... , 2 types, 2 molecules AC
#3: Protein | Mass: 16929.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein | Mass: 17182.756 Da / Num. of mol.: 1 / Mutation: C87K, K92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P61088, E2 ubiquitin-conjugating enzyme |
-Non-polymers , 2 types, 287 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop Details: MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2019 / Details: Eiger2 XE 16M |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.99 Å / Num. obs: 38727 / % possible obs: 99.41 % / Redundancy: 7.1 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04551 / Rpim(I) all: 0.01839 / Rrim(I) all: 0.04914 / Net I/σ(I): 20.18 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.9457 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 3856 / CC1/2: 0.932 / % possible all: 99.15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6S53, 1UBQ, 1J74 Resolution: 2.2→19.99 Å / SU ML: 0.2935 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6248 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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