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- PDB-7v8f: Crystal structure of UBE2L3 bound to HOIP RING1 domain. -

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Basic information

Entry
Database: PDB / ID: 7v8f
TitleCrystal structure of UBE2L3 bound to HOIP RING1 domain.
Components
  • E3 ubiquitin-protein ligase RNF31
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsLIGASE / E3 liagse / ubiquitin / innate immune
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / cell cycle phase transition / ubiquitin-protein transferase activator activity / positive regulation of xenophagy / CD40 receptor complex / protein K11-linked ubiquitination ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / cell cycle phase transition / ubiquitin-protein transferase activator activity / positive regulation of xenophagy / CD40 receptor complex / protein K11-linked ubiquitination / negative regulation of necroptotic process / cellular response to glucocorticoid stimulus / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of ubiquitin-protein transferase activity / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / transcription coactivator activity / protein ubiquitination / defense response to bacterium / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair ...: / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 L3 / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLiu, J. / Wang, Y. / Pan, L.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071297 China
National Natural Science Foundation of China (NSFC)21822705 China
National Natural Science Foundation of China (NSFC)91753113 China
National Natural Science Foundation of China (NSFC)21621002 China
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri.
Authors: Liu, J. / Wang, Y. / Wang, D. / Wang, Y. / Xu, X. / Zhang, Y. / Li, Y. / Zhang, M. / Gong, X. / Tang, Y. / Shen, L. / Li, M. / Pan, L.
History
DepositionAug 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: E3 ubiquitin-protein ligase RNF31
A: Ubiquitin-conjugating enzyme E2 L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9564
Polymers29,8252
Non-polymers1312
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, 1:1 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-10 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.097, 108.412, 37.156
Angle α, β, γ (deg.)90.000, 106.328, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 11637.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase
#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: 18187.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8
Details: 2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(w/v) PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.66→108.41 Å / Num. obs: 24757 / % possible obs: 91.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.71 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.014 / Net I/σ(I): 30.4
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 1078 / CC1/2: 0.959 / Rpim(I) all: 0.13 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS20190806data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q5H

4q5h


Resolution: 1.66→54.21 Å / SU ML: 0.1437 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.3252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198 1158 4.68 %
Rwork0.1753 23564 -
obs0.1763 24722 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.76 Å2
Refinement stepCycle: LAST / Resolution: 1.66→54.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 2 192 2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882016
X-RAY DIFFRACTIONf_angle_d1.06992739
X-RAY DIFFRACTIONf_chiral_restr0.0541308
X-RAY DIFFRACTIONf_plane_restr0.0073352
X-RAY DIFFRACTIONf_dihedral_angle_d15.946273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.740.2131390.18252734X-RAY DIFFRACTION86.2
1.74-1.830.23541670.18743123X-RAY DIFFRACTION98.21
1.83-1.940.24061380.19282879X-RAY DIFFRACTION88.84
1.94-2.090.21371140.19382444X-RAY DIFFRACTION76.61
2.09-2.30.2291580.18952809X-RAY DIFFRACTION87.68
2.3-2.630.23061460.19363207X-RAY DIFFRACTION99.91
2.64-3.320.22911450.18613232X-RAY DIFFRACTION99.76
3.32-54.210.15121510.1533136X-RAY DIFFRACTION96.68

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