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- PDB-8st8: Structure of E3 ligase SopA bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8st8
TitleStructure of E3 ligase SopA bound to ubiquitin
Components
  • E3 ubiquitin-protein ligase SopA
  • Ubiquitin
KeywordsTRANSFERASE / E3 ubiquitin ligase / LIGASE
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / 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 ...HECT-type E3 ubiquitin transferase / 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
Similarity search - Function
effector protein (NleL) fold / effector protein (NleL) / E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. ...effector protein (NleL) fold / effector protein (NleL) / E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / 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 / Polyubiquitin-C / E3 ubiquitin-protein ligase SopA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SopA
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5953
Polymers30,5372
Non-polymers571
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-3 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.893, 63.644, 81.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase SopA / HECT-type E3 ubiquitin transferase SopA / Salmonella outer protein A / Secreted effector protein SopA


Mass: 22017.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sopA, STM2066 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZNR3, HECT-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 22.5% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 7.0, and 20% glycerol

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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: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→36.06 Å / Num. obs: 27443 / % possible obs: 98.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / Num. unique obs: 1493 / CC1/2: 0.739 / % possible all: 98.1

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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: 1.75→36.06 Å / SU ML: 0.1771 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1963 2575 4.98 %
Rwork0.1765 49119 -
obs0.1775 27443 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 4 218 2348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672221
X-RAY DIFFRACTIONf_angle_d0.85733019
X-RAY DIFFRACTIONf_chiral_restr0.0556336
X-RAY DIFFRACTIONf_plane_restr0.0064394
X-RAY DIFFRACTIONf_dihedral_angle_d15.1022809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.32541470.28942737X-RAY DIFFRACTION97.6
1.78-1.820.31361390.26372590X-RAY DIFFRACTION94.69
1.82-1.860.2321420.25112761X-RAY DIFFRACTION98.24
1.86-1.90.25541580.2372724X-RAY DIFFRACTION99.48
1.9-1.950.21961410.21962745X-RAY DIFFRACTION99.21
1.95-20.19081490.19982753X-RAY DIFFRACTION99.01
2-2.060.19731290.1822758X-RAY DIFFRACTION98.77
2.06-2.130.18861330.18432702X-RAY DIFFRACTION97.86
2.13-2.20.15351460.17072648X-RAY DIFFRACTION95.95
2.21-2.290.19391540.17882764X-RAY DIFFRACTION99.73
2.29-2.40.23441410.17062776X-RAY DIFFRACTION99.83
2.4-2.520.21641520.17872748X-RAY DIFFRACTION99.25
2.52-2.680.1951480.17682734X-RAY DIFFRACTION99.14
2.68-2.890.15851250.17852710X-RAY DIFFRACTION96.43
2.89-3.180.21741420.17362746X-RAY DIFFRACTION99.65
3.18-3.640.17741100.15322769X-RAY DIFFRACTION99.07
3.64-4.580.18171470.14122744X-RAY DIFFRACTION98.17
4.58-36.060.18641720.18482710X-RAY DIFFRACTION99

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