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- PDB-8eb0: RNF216/E2-Ub/Ub transthiolation complex -

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Basic information

Entry
Database: PDB / ID: 8eb0
TitleRNF216/E2-Ub/Ub transthiolation complex
Components
  • E3 ubiquitin-protein ligase RNF216
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsLIGASE / ubiquitin / transthiolation / ZF / RBR
Function / homology
Function and homology information


regulation of interferon-beta production / cell cycle phase transition / ubiquitin-protein transferase activator activity / regulation of defense response to virus by host / protein K11-linked ubiquitination / clathrin-coated vesicle / positive regulation of protein targeting to mitochondrion / negative regulation of type I interferon production / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme ...regulation of interferon-beta production / cell cycle phase transition / ubiquitin-protein transferase activator activity / regulation of defense response to virus by host / protein K11-linked ubiquitination / clathrin-coated vesicle / positive regulation of protein targeting to mitochondrion / negative regulation of type I interferon production / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling
Similarity search - Function
: / : / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin-conjugating enzyme, active site ...: / : / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 L3 / E3 ubiquitin-protein ligase RNF216
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsCotton, T.R. / Wang, X.S. / Lechtenberg, B.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1182757 Australia
Citation
Journal: Nat Commun / Year: 2023
Title: The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family.
Authors: Wang, X.S. / Cotton, T.R. / Trevelyan, S.J. / Richardson, L.W. / Lee, W.T. / Silke, J. / Lechtenberg, B.C.
#1: Journal: Biorxiv / Year: 2022
Title: The unifying catalytic mechanism of the RING-between-RING E3 ligase family
Authors: Wang, X.S. / Cotton, T.R. / Trevelyan, S.J. / Richardson, L.W. / Lee, W.T. / Silke, J. / Lechtenberg, B.C.
History
DepositionAug 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: E3 ubiquitin-protein ligase RNF216
B: Ubiquitin-conjugating enzyme E2 L3
C: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,57914
Polymers66,8334
Non-polymers74610
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-56 kcal/mol
Surface area27320 Å2
Unit cell
Length a, b, c (Å)152.545, 70.363, 65.152
Angle α, β, γ (deg.)90.000, 108.700, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein E3 ubiquitin-protein ligase RNF216 / RING finger protein 216 / RING-type E3 ubiquitin transferase RNF216 / Triad domain-containing ...RING finger protein 216 / RING-type E3 ubiquitin transferase RNF216 / Triad domain-containing protein 3 / Ubiquitin-conjugating enzyme 7-interacting protein 1 / Zinc finger protein inhibiting NF-kappa-B


Mass: 31552.082 Da / Num. of mol.: 1 / Mutation: C688A
Source method: isolated from a genetically manipulated source
Details: S719 is phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: RNF216, TRIAD3, UBCE7IP1, ZIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NWF9
#2: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 18126.848 Da / Num. of mol.: 1 / Mutation: C86K
Source method: isolated from a genetically manipulated source
Details: C86K forms an isopeptide bond with ubiquitin G76 in chain C.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68036
#3: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The ubiquitin C-terminus of chain C forms an isopeptide bond with UbcH7 C86K in chain B.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.03→47.64 Å / Num. obs: 12690 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 82.79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.111 / Χ2: 0.55 / Net I/σ(I): 5.6
Reflection shellResolution: 3.03→3.21 Å / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1986 / CC1/2: 0.533 / Χ2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSNov 1, 2016 BUILT=20161205data reduction
Aimlessversion 0.7.4data scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 7M4O, 1UBQ, 4Q5E, & 7M4M, AlphaFold model

7m4o

1ubq

4q5e

7m4m


Resolution: 3.03→41.37 Å / SU ML: 0.582 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.1913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3389 1267 10 %
Rwork0.3026 11400 -
obs0.3062 12667 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.44 Å2
Refinement stepCycle: LAST / Resolution: 3.03→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 22 0 4423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194490
X-RAY DIFFRACTIONf_angle_d0.48596041
X-RAY DIFFRACTIONf_chiral_restr0.0409659
X-RAY DIFFRACTIONf_plane_restr0.0046786
X-RAY DIFFRACTIONf_dihedral_angle_d11.20631759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.150.38961320.42081180X-RAY DIFFRACTION93.31
3.15-3.290.43261430.38331294X-RAY DIFFRACTION99.65
3.29-3.460.33631430.34921280X-RAY DIFFRACTION99.58
3.46-3.680.39031400.34191274X-RAY DIFFRACTION99.37
3.68-3.960.33451400.33051252X-RAY DIFFRACTION98.31
3.96-4.360.3631430.30981286X-RAY DIFFRACTION98.82
4.36-4.990.35461400.28391260X-RAY DIFFRACTION97.63
4.99-6.280.29371410.30371270X-RAY DIFFRACTION98.4
6.29-41.370.30581450.24291304X-RAY DIFFRACTION97.12
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3556289293310.1706875080210.105603410210.8546119873960.8525655248660.8227051946520.01510381267830.180384508852-0.0180220896213-0.5885042419280.1761478164940.0747738450987-1.291910152350.3308343897380.01833207686160.8668712373870.0558677350783-0.07804336504540.646825903299-0.05604677456080.7184520291-30.774839585536.2679926354-3.51224458924
20.4121633987520.115762160593-0.3718303157750.304306346935-0.04188127526970.3203973319430.278756696629-0.3729120997180.324763317211-0.1670097815480.051182787017-0.368608639495-0.284532111433-0.358475282923-0.0003253883111651.040726534670.07171822809850.3198420569690.8557239502070.02074042488520.807217833635-50.114921198232.478730462227.7353536333
30.3905401784710.6295694174611.044312916272.186082647810.6443356891991.79786642089-0.0629428351720.0231319433423-0.004952023817050.50191297623-0.0612067438519-0.20088792866-0.1580046436720.067303769135-6.50971694477E-50.6453398529370.005799918510680.1359016178340.7669857483210.05079285907430.67971369842-31.856262938427.0236295486.75273305338
40.924624393472-0.296405903583-0.7615039863140.2185106500260.2733353721010.7160358953060.195332436468-0.207189098588-0.729368233903-0.1207196999870.5570881491440.5121313637990.7934052472640.2942786426260.0002792157424181.256702622830.196869919836-0.3293923078581.213019327080.08332019770951.30908144706-3.4919176977420.256334562817.2333824972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'C' and resid 1 through 76)CJ1 - 761 - 76
22(chain 'D' and resid 1 through 73)DK1 - 731 - 73
33(chain 'A' and resid 512 through 772)AA512 - 7721 - 255
44(chain 'B' and resid 1 through 146)BI1 - 1461 - 146

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