+Open data
-Basic information
Entry | Database: PDB / ID: 6m2d | ||||||
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Title | MUL1-RING domain | ||||||
Components | Mitochondrial ubiquitin ligase activator of NFKB 1 | ||||||
Keywords | TRANSFERASE / MUL1 / 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 / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / negative regulation of mitochondrial fusion / mitochondrion localization / positive regulation of protein sumoylation / positive regulation of dendrite extension / mitochondrial fission / regulation of mitochondrion organization ...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 / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / negative regulation of mitochondrial fusion / mitochondrion localization / positive regulation of protein sumoylation / positive regulation of dendrite extension / mitochondrial fission / regulation of mitochondrion organization / SUMO transferase activity / negative regulation of type I interferon-mediated signaling pathway / positive regulation of mitochondrial fission / cellular response to exogenous dsRNA / protein sumoylation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of innate immune response / regulation of mitochondrial membrane potential / protein destabilization / RING-type E3 ubiquitin transferase / negative regulation of cell growth / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / p53 binding / Neddylation / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / protein stabilization / protein ubiquitination / Ub-specific processing proteases / axon / neuronal cell body / apoptotic process / ubiquitin protein ligase binding / mitochondrion / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å | ||||||
Authors | Lee, S.O. / Ryu, K.S. / Chi, S.-W. | ||||||
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 | 6m2d.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2d.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 6m2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2d ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2d | HTTPS FTP |
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-Related structure data
Related structure data | 6m2cC 7bolC 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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-Components
#1: Protein | Mass: 6251.479 Da / Num. of mol.: 6 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 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #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 grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.4 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350 |
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-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: 1.2837 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2837 Å / Relative weight: 1 |
Reflection | Resolution: 1.795→50 Å / Num. obs: 25501 / % possible obs: 96.8 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.026 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.8→10 Å / Num. unique obs: 25501 / Rpim(I) all: 0.026 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T6P Resolution: 1.795→47.671 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.45 Å2 / Biso mean: 23.5384 Å2 / Biso min: 11.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.795→47.671 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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