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- PDB-8st7: Structure of E3 ligase VsHECT bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8st7
TitleStructure of E3 ligase VsHECT bound to ubiquitin
Components
  • E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein
  • Ubiquitin
KeywordsTRANSFERASE / E3 ubiquitin ligase / LIGASE
Function / homology
Function and homology information


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 ...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 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / 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 / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Assembly Of The HIV Virion
Similarity search - Function
effector protein (NleL) fold / effector protein (NleL) / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / Pentapeptide repeat region / : / Pentapeptide repeat / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : ...effector protein (NleL) fold / effector protein (NleL) / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / Pentapeptide repeat region / : / Pentapeptide repeat / 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 / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Verrucomicrobiota (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsFranklin, T.G. / Pruneda, J.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142486 United States
Citation
Journal: Mol.Cell / Year: 2023
Title: Bacterial ligases reveal fundamental principles of polyubiquitin specificity.
Authors: Franklin, T.G. / Brzovic, P.S. / Pruneda, J.N.
#1: Journal: Biorxiv / Year: 2023
Title: Bacterial mimicry of eukaryotic HECT ubiquitin ligation.
Authors: Franklin, T.G. / Brzovic, P.S. / Pruneda, J.N.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Jan 3, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Ubiquitin
B: Ubiquitin
A: E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein
C: E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3776
Polymers69,2634
Non-polymers1142
Water9,728540
1
D: Ubiquitin
C: E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6893
Polymers34,6312
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
A: E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6893
Polymers34,6312
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.855, 157.276, 53.025
Angle α, β, γ (deg.)90.000, 93.756, 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 Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein E3 ubiquitin-protein ligase SopA-like catalytic domain-containing protein


Mass: 26111.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucomicrobiota (bacteria) / Gene: C5B47_04425 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2RSR1
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.16 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 2K MME, 0.1 M MES pH 6.0, and 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.44→39.32 Å / Num. obs: 91269 / % possible obs: 86.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Net I/σ(I): 17.7
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2146 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
Web-Icedata collection
XDSdata reduction
AimlessCCP4-7.1.015data scaling
PHASERCCP4-7.1.015phasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→37.24 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1985 8719 4.88 %
Rwork0.1701 169831 -
obs0.1714 91220 85.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.71 Å2
Refinement stepCycle: LAST / Resolution: 1.44→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 8 540 5129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01164722
X-RAY DIFFRACTIONf_angle_d1.25686368
X-RAY DIFFRACTIONf_chiral_restr0.0831721
X-RAY DIFFRACTIONf_plane_restr0.0114822
X-RAY DIFFRACTIONf_dihedral_angle_d15.44581852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.3541620.30962526X-RAY DIFFRACTION39.5
1.46-1.470.26911400.27922858X-RAY DIFFRACTION42.66
1.47-1.490.26481740.26393164X-RAY DIFFRACTION47.32
1.49-1.510.30351880.26223475X-RAY DIFFRACTION52.78
1.51-1.530.2181960.23693911X-RAY DIFFRACTION59.22
1.53-1.550.27332460.23214237X-RAY DIFFRACTION63.83
1.55-1.570.26052180.22424861X-RAY DIFFRACTION73.49
1.57-1.60.26333140.22795731X-RAY DIFFRACTION86.23
1.6-1.620.24893240.21836090X-RAY DIFFRACTION92.12
1.62-1.650.23543050.20886319X-RAY DIFFRACTION95.19
1.65-1.680.23343080.20326368X-RAY DIFFRACTION95.41
1.68-1.710.2343200.20716282X-RAY DIFFRACTION93.43
1.71-1.740.24213580.2076235X-RAY DIFFRACTION96.21
1.74-1.780.23053250.20226320X-RAY DIFFRACTION94.42
1.78-1.810.20863120.19386021X-RAY DIFFRACTION91.35
1.81-1.860.20033230.19096186X-RAY DIFFRACTION93.76
1.86-1.90.20113150.18326398X-RAY DIFFRACTION95.23
1.9-1.950.18793280.17516409X-RAY DIFFRACTION96.91
1.95-2.010.22143170.17856330X-RAY DIFFRACTION95.11
2.01-2.080.19693230.17386318X-RAY DIFFRACTION96.09
2.08-2.150.19562810.16356419X-RAY DIFFRACTION95.48
2.15-2.240.1763150.16386125X-RAY DIFFRACTION91.18
2.24-2.340.17582860.15486383X-RAY DIFFRACTION96.95
2.34-2.460.20243310.1566450X-RAY DIFFRACTION97.34
2.46-2.620.16743450.1576460X-RAY DIFFRACTION97.28
2.62-2.820.19953260.15766198X-RAY DIFFRACTION93.28
2.82-3.10.1953560.1666456X-RAY DIFFRACTION98.04
3.1-3.550.21683650.15896534X-RAY DIFFRACTION98.43
3.55-4.470.1723270.14036310X-RAY DIFFRACTION95.1
4.47-37.240.16772910.16636457X-RAY DIFFRACTION97.02

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