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- PDB-6k2k: Solution structure of MUL1-RING domain -

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Basic information

Entry
Database: PDB / ID: 6k2k
TitleSolution structure of MUL1-RING domain
ComponentsMitochondrial ubiquitin ligase activator of NFKB 1
KeywordsSTRUCTURAL PROTEIN / Solution structure / E3 ubiquitin ligase
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
E3 Ubiquitin ligase MUL1-like / E3 Ubiquitin ligase / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitochondrial ubiquitin ligase activator of NFKB 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLee, M.S. / Lee, M.K. / Ryu, K.S. / Chi, S.W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Solution structure of MUL1-RING domain and its interaction with p53 transactivation domain.
Authors: Lee, M.S. / Lee, S.O. / Lee, M.K. / Yi, G.S. / Lee, C.K. / Ryu, K.S. / Chi, S.W.
History
DepositionMay 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3823
Polymers6,2511
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3850 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Mitochondrial ubiquitin ligase activator of NFKB 1 / E3 SUMO-protein ligase MUL1 / E3 ubiquitin-protein ligase MUL1 / Growth inhibition and death E3 ...E3 SUMO-protein ligase MUL1 / E3 ubiquitin-protein ligase MUL1 / Growth inhibition and death E3 ligase / Mitochondrial-anchored protein ligase / MAPL / Putative NF-kappa-B-activating protein 266 / RING finger protein 218 / RING-type E3 ubiquitin transferase NFKB 1


Mass: 6251.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUL1, C1orf166, GIDE, MAPL, MULAN, RNF218 / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q969V5, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D (H)CCH-TOCSY
171isotropic13D CCH-TOCSY
181isotropic13D (H)CCH-COSY
191isotropic13D CC(CO)NH
1101isotropic13D HBHA(CO)NH
1111isotropic13D (HB)CB(CGCD)HD
1121isotropic13D HBCBCGCDHDHE
1131isotropic13D NOESY
1141anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.9 mM [U-99% 13C; U-99% 15N] Mitochondrial ubiquitin ligase activator of NFKB 1, 90% H2O/10% D2O
Details: 13C, 15N-labeled MUL1-RING domain / Label: 13C, 15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.9 mM
Component: Mitochondrial ubiquitin ligase activator of NFKB 1
Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 50 mM MES, pH 6.5, 50 mM NaCl, 5 microM Zinc sulfate, 10 mM dithiothreitol (DTT), and 10 % (v/v) D2O
Ionic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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