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Yorodumi- PDB-5v1z: Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v1z | |||||||||
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Title | Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex | |||||||||
Components |
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Keywords | PROTEIN BINDING / RPN13 / proteasome / RPN2 / ubiquitin | |||||||||
Function / homology | Function and homology information proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / Regulation of ornithine decarboxylase (ODC) / female meiosis I / positive regulation of protein monoubiquitination / Cross-presentation of soluble exogenous antigens (endosomes) / mitochondrion transport along microtubule ...proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / Regulation of ornithine decarboxylase (ODC) / female meiosis I / positive regulation of protein monoubiquitination / Cross-presentation of soluble exogenous antigens (endosomes) / mitochondrion transport along microtubule / fat pad development / Somitogenesis / molecular function inhibitor activity / proteasome binding / female gonad development / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / proteasome storage granule / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endopeptidase activator activity / proteasome assembly / enzyme regulator activity / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / proteasome complex / 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 / EGFR downregulation / 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 / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hemmis, C.W. / VanderLinden, R.T. / Yao, T. / Robinson, H. / Hill, C.P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. Authors: VanderLinden, R.T. / Hemmis, C.W. / Yao, T. / Robinson, H. / Hill, C.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v1z.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v1z.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 5v1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v1z_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 5v1z_full_validation.pdf.gz | 473.4 KB | Display | |
Data in XML | 5v1z_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5v1z_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/5v1z ftp://data.pdbj.org/pub/pdb/validation_reports/v1/5v1z | HTTPS FTP |
-Related structure data
Related structure data | 5v1yC 1cmxS 2r2yS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13482.367 Da / Num. of mol.: 2 / Fragment: PRU domain (UNP residues 19-132) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADRM1, GP110 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: Q16186 #2: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET3a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: P0CG47 #3: Protein/peptide | Mass: 2617.699 Da / Num. of mol.: 2 / Fragment: C-termimal domain (UNP residues 932-953) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIL / References: UniProt: Q99460 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, pH 4.6, 22.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 28875 / % possible obs: 100 % / Redundancy: 4.7 % / Rsym value: 0.098 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2748 / Num. unique obs: 2748 / Rsym value: 0.628 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2R2Y & 1CMX Resolution: 2→33.012 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.012 Å
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Refine LS restraints |
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LS refinement shell |
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