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- PDB-6m2c: Distinct mechanism of MUL1-RING domain simultaneously recruiting ... -

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Basic information

Entry
Database: PDB / ID: 6m2c
TitleDistinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain
Components
  • Mitochondrial ubiquitin ligase activator of NFKB 1
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsTRANSFERASE / 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 / positive regulation of dendrite extension / positive regulation of protein sumoylation / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of type 2 mitophagy / mitochondrial fission ...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 / positive regulation of dendrite extension / positive regulation of protein sumoylation / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of type 2 mitophagy / 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 / protein K48-linked ubiquitination / protein autoubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Inactivation of CSF3 (G-CSF) signaling / protein destabilization / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein modification process / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / p53 binding / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / peroxisome / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / 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 / protein-containing complex / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
E3 Ubiquitin ligase MUL1-like / E3 Ubiquitin ligase / : / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...E3 Ubiquitin ligase MUL1-like / E3 Ubiquitin ligase / : / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 / Mitochondrial ubiquitin ligase activator of NFKB 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsLee, S.O. / Ryu, K.S. / Chi, S.-W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Korea) Korea, Republic Of
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 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 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin-conjugating enzyme E2 D2
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin-conjugating enzyme E2 D2
E: Mitochondrial ubiquitin ligase activator of NFKB 1
F: Mitochondrial ubiquitin ligase activator of NFKB 1
G: Mitochondrial ubiquitin ligase activator of NFKB 1
H: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55016
Polymers92,0278
Non-polymers5238
Water1,11762
1
A: Ubiquitin-conjugating enzyme E2 D2
E: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1384
Polymers23,0072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 D2
F: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1384
Polymers23,0072
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2 D2
G: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1384
Polymers23,0072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-conjugating enzyme E2 D2
H: Mitochondrial ubiquitin ligase activator of NFKB 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1384
Polymers23,0072
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.207, 141.241, 68.047
Angle α, β, γ (deg.)90.000, 104.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C
41chain D and segid D
12chain E and segid E
22chain F and segid F
32chain G and segid G
42chain H and segid H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0
411chain D and segid DD0
112chain E and segid EE0
212chain F and segid FF0
312chain G and segid GG0
412chain H and segid HH0

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


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
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: 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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 4% v/v Tacsimate pH 6.0, 12% 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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.830.28717680.6180.1710.3371.06474.8
2.8-2.913.20.25918460.7540.1490.3011.16879
2.91-3.043.60.21919060.8720.1160.2491.30981.3
3.04-3.23.90.19320060.9210.0980.2181.53285.5
3.2-3.44.50.15321180.9640.0740.171.74889.3
3.4-3.664.90.12121700.9820.0560.1342.05792.5
3.66-4.035.60.09323090.990.0410.1022.3997.4
4.03-4.626.50.07223300.9950.030.0782.42899.5
4.62-5.8170.06623590.9960.0270.0722.45699.7
5.81-506.90.05423880.9980.0220.0592.88899.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T6P, 2ESK

3t6p

2esk


Resolution: 2.702→45.639 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.2583 2000 9.44 %
Rwork0.2116 --
obs0.2159 21183 89.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.97 Å2 / Biso mean: 41.6533 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 2.702→45.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 8 62 6499
Biso mean--33.42 34.87 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066605
X-RAY DIFFRACTIONf_angle_d1.2928986
X-RAY DIFFRACTIONf_chiral_restr0.046992
X-RAY DIFFRACTIONf_plane_restr0.0061157
X-RAY DIFFRACTIONf_dihedral_angle_d13.3612485
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2781X-RAY DIFFRACTION11.914TORSIONAL
12B2781X-RAY DIFFRACTION11.914TORSIONAL
13C2781X-RAY DIFFRACTION11.914TORSIONAL
14D2781X-RAY DIFFRACTION11.914TORSIONAL
21E1004X-RAY DIFFRACTION11.914TORSIONAL
22F1004X-RAY DIFFRACTION11.914TORSIONAL
23G1004X-RAY DIFFRACTION11.914TORSIONAL
24H1004X-RAY DIFFRACTION11.914TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.702-2.76930.36321150.3121110272
2.7693-2.84420.35961220.2806116978
2.8442-2.92790.3471260.2805121579
2.9279-3.02230.31151280.2586122481
3.0223-3.13030.3251340.2565128884
3.1303-3.25560.30391400.2463133388
3.2556-3.40380.25431420.2325137689
3.4038-3.58320.28121460.223139291
3.5832-3.80750.23531510.2027145896
3.8075-4.10140.2451550.1892148098
4.1014-4.51380.21451600.16921537100
4.5138-5.16610.21351600.16621541100
5.1661-6.50580.25131600.19461524100
6.5058-70.22581610.2056154499

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