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Yorodumi- PDB-6m2c: Distinct mechanism of MUL1-RING domain simultaneously recruiting ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2c | ||||||
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Title | Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain | ||||||
Components |
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Keywords | TRANSFERASE / MUL1-RING / Ube2d2 / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of chemokine (C-C motif) ligand 5 production / negative regulation of defense response to virus by host / : / negative regulation of mitochondrial fusion / mitochondrion localization / ubiquitin conjugating enzyme complex / positive regulation of protein sumoylation / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of dendrite extension ...regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of chemokine (C-C motif) ligand 5 production / negative regulation of defense response to virus by host / : / negative regulation of mitochondrial fusion / mitochondrion localization / ubiquitin conjugating enzyme complex / positive regulation of protein sumoylation / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of dendrite extension / mitochondrial fission / regulation of mitochondrion organization / SUMO transferase activity / negative regulation of type I interferon-mediated signaling pathway / E2 ubiquitin-conjugating enzyme / positive regulation of mitochondrial fission / cellular response to exogenous dsRNA / ubiquitin conjugating enzyme activity / protein sumoylation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / negative regulation of innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / protein destabilization / RING-type E3 ubiquitin transferase / negative regulation of cell growth / protein modification process / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / : / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / p53 binding / Antigen processing: Ubiquitination & Proteasome degradation / peroxisome / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / protein stabilization / Ub-specific processing proteases / protein ubiquitination / axon / neuronal cell body / ubiquitin protein ligase binding / apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å | ||||||
Authors | Lee, S.O. / Ryu, K.S. / Chi, S.-W. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Febs J. / Year: 2022 Title: MUL1-RING recruits the substrate, p53-TAD as a complex with UBE2D2-UB conjugate. Authors: Lee, M.S. / Lee, S.O. / Choi, J. / Ryu, M. / Lee, M.K. / Kim, J.H. / Hwang, E. / Lee, C.K. / Chi, S.W. / Ryu, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m2c.cif.gz | 299.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2c.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m2c_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 6m2c_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 6m2c_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 6m2c_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2c ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2c | HTTPS FTP |
-Related structure data
Related structure data | 6m2dC 7bolC 2eskS 3t6pS S: Starting model for refinement C: citing same article (ref.) |
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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:
NCS ensembles :
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-Components
#1: Protein | Mass: 16899.357 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme #2: Protein | Mass: 6107.350 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MUL1, C1orf166, GIDE, MAPL, MULAN, RNF218 / Production host: Escherichia coli (E. coli) References: UniProt: Q969V5, RING-type E3 ubiquitin transferase #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 21200 / % possible obs: 89.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 40.22 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Χ2: 2.167 / Net I/σ(I): 13.2 / Num. measured all: 107188 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T6P, 2ESK Resolution: 2.702→45.639 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 25.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.97 Å2 / Biso mean: 41.6533 Å2 / Biso min: 10.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.702→45.639 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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