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- PDB-6m2d: MUL1-RING domain -

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Basic information

Entry
Database: PDB / ID: 6m2d
TitleMUL1-RING domain
ComponentsMitochondrial ubiquitin ligase activator of NFKB 1
KeywordsTRANSFERASE / 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 / negative regulation of mitochondrial fusion / positive regulation of dendrite extension / positive regulation of protein sumoylation / mitochondrion localization / positive regulation of type 2 mitophagy / 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 / negative regulation of mitochondrial fusion / positive regulation of dendrite extension / positive regulation of protein sumoylation / mitochondrion localization / positive regulation of type 2 mitophagy / 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 / RING-type E3 ubiquitin transferase / protein destabilization / protein polyubiquitination / ubiquitin-protein transferase activity / p53 binding / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / peroxisome / Neddylation / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / protein stabilization / protein ubiquitination / axon / neuronal cell body / apoptotic process / ubiquitin protein ligase binding / mitochondrion / zinc ion binding / identical protein binding / membrane
Similarity search - Function
E3 Ubiquitin ligase MUL1-like / E3 Ubiquitin ligase / : / Zinc finger, C3HC4 type (RING finger) / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Mitochondrial ubiquitin ligase activator of NFKB 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å
AuthorsLee, S.O. / Ryu, K.S. / Chi, S.-W.
CitationJournal: 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
DepositionFeb 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Mitochondrial ubiquitin ligase activator of NFKB 1
C: Mitochondrial ubiquitin ligase activator of NFKB 1
D: Mitochondrial ubiquitin ligase activator of NFKB 1
E: Mitochondrial ubiquitin ligase activator of NFKB 1
F: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,87024
Polymers37,5096
Non-polymers1,36118
Water5,621312
1
A: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5745
Polymers6,2511
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5745
Polymers6,2511
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4784
Polymers6,2511
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3823
Polymers6,2511
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4784
Polymers6,2511
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3823
Polymers6,2511
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.226, 66.593, 68.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 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

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.2837 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2837 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.8→10 Å / Num. unique obs: 25501 / Rpim(I) all: 0.026

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T6P

3t6p


Resolution: 1.795→47.671 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.84
RfactorNum. reflection% reflection
Rfree0.2272 1287 5.05 %
Rwork0.1716 --
obs0.1744 25501 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.45 Å2 / Biso mean: 23.5384 Å2 / Biso min: 11.09 Å2
Refinement stepCycle: final / Resolution: 1.795→47.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 42 312 2911
Biso mean--42.57 30.1 -
Num. residues----338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7951-1.8670.32291310.2793247392
1.867-1.9520.26391260.2383265798
1.952-2.05490.26581600.2163264899
2.0549-2.18360.26171540.1844264399
2.1836-2.35220.22081350.1722270599
2.3522-2.58890.25561420.17362703100
2.5889-2.96350.23761350.17612754100
2.9635-3.73350.23071450.14382748100
3.7335-100.17441590.14522883100

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