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- PDB-4bvu: Structure of Shigella effector OspG in complex with host UbcH5c- ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bvu | ||||||
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Title | Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate | ||||||
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![]() | TRANSFERASE/LIGASE/PROTEIN BINDING / TRANSFERASE-LIGASE-PROTEIN BINDING COMPLEX / KINASE | ||||||
Function / homology | ![]() Transferases; Transferring phosphorus-containing groups / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / : ...Transferases; Transferring phosphorus-containing groups / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / : / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Degradation of AXIN / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pruneda, J.N. / LeTrong, I. / Stenkamp, R.E. / Klevit, R.E. / Brzovic, P.S. | ||||||
![]() | ![]() Title: E2~Ub Conjugates Regulate the Kinase Activity of Shigella Effector Ospg During Pathogenesis. Authors: Pruneda, J.N. / Smith, F.D. / Daurie, A. / Swaney, D.L. / Villen, J. / Scott, J.D. / Stadnyk, A.W. / Le Trong, I. / Stenkamp, R.E. / Klevit, R.E. / Rohde, J.R. / Brzovic, P.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.8 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1x23S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24390.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q99PZ6, Transferases; Transferring phosphorus-containing groups |
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#2: Protein | Mass: 16690.068 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: OXYESTER LINK BETWEEN S85 AND UBIQUITIN G76 / Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: OXYESTER LINK BETWEEN G76 AND UBCH5C S85 / Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.32 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M TRIS PH 8.5, 20% ETOH |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 17947 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.1 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 16.39 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.58 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X23 Resolution: 2.7→44.16 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.859 / SU B: 13.298 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.907 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→44.16 Å
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