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Yorodumi- PDB-3mhs: Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to u... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mhs | ||||||
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Title | Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde | ||||||
Components |
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Keywords | Hydrolase/transcription regulator/protein binding / Multi-protein complex / Hydrolase-transcription regulator-protein binding complex / Acetylation / Cytoplasm / Isopeptide bond / Nucleus / Phosphoprotein / Ubl conjugation | ||||||
Function / homology | Function and homology information RITS complex assembly / DUBm complex / : / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / protein modification process => GO:0036211 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex ...RITS complex assembly / DUBm complex / : / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / protein modification process => GO:0036211 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Ub-specific processing proteases / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / enzyme activator activity / mRNA export from nucleus / nuclear pore / cytosolic ribosome / 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 / Membrane binding and targetting of GAG proteins / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / RNA splicing / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å | ||||||
Authors | Samara, N.L. / Datta, A.B. / Berndsen, C.E. / Zhang, X. / Yao, T. / Cohen, R.E. / Wolberger, C. | ||||||
Citation | Journal: Science / Year: 2010 Title: Structural insights into the assembly and function of the SAGA deubiquitinating module. Authors: Samara, N.L. / Datta, A.B. / Berndsen, C.E. / Zhang, X. / Yao, T. / Cohen, R.E. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mhs.cif.gz | 376.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mhs.ent.gz | 317.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mhs ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mhs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 54033.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBP8, YMR223W, YM9959.05 / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: P50102, EC: 3.1.2.15 |
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#2: Protein | Mass: 11094.497 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SUS1, YBR111W-A / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: Q6WNK7 |
#4: Protein | Mass: 8560.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA52, UBB, UBC / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: P62988, UniProt: P0CG48*PLUS |
-SAGA-associated factor ... , 2 types, 2 molecules CE
#3: Protein | Mass: 11297.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SGF11, YPL047W / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: Q03067 |
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#5: Protein | Mass: 10824.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SGF73, YGL066W / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: P53165 |
-Non-polymers , 4 types, 855 molecules
#6: Chemical | ChemComp-EDO / | ||
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#7: Chemical | ChemComp-GOL / | ||
#8: Chemical | ChemComp-ZN / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % Description: THE INITIAL STRUCTURE WAS DETERMINED WITH 3 WAVELENGTH SE-MAD USING THE FOLLOWING WAVELENGTHS (EV): PEAK: 12658.7 HIGH REMOTE: 13058.7 INFLECTION: 12656.9 THE STRUCTURE WAS THEN REFINED ...Description: THE INITIAL STRUCTURE WAS DETERMINED WITH 3 WAVELENGTH SE-MAD USING THE FOLLOWING WAVELENGTHS (EV): PEAK: 12658.7 HIGH REMOTE: 13058.7 INFLECTION: 12656.9 THE STRUCTURE WAS THEN REFINED AGAINST A NATIVE DATA SET COLLECTED AT A WAVELENGTH OF 13058.7 (EV). THE FINAL COORDINATES REPRESENT THE NATIVE DATA SET. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94944 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2010 Details: K-B pair of biomorph mirrors with two additional horizontally deflecting mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94944 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→35.1 Å / Num. all: 78011 / Num. obs: 73928 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.886 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.89→35.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.921 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.127 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.086 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→35.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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