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Yorodumi- PDB-2pe9: NMR Based Structure of the Open Conformation of LYS48-Linked Di-U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pe9 | ||||||
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Title | NMR Based Structure of the Open Conformation of LYS48-Linked Di-UBiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements | ||||||
Components | Ubiquitin | ||||||
Keywords | SIGNALING PROTEIN / UBIQUITIN / LYS48-LINKED POLYUBIQUITIN / POLYUBIQUITIN | ||||||
Function / homology | Function and homology information : / : / protein modification process => GO:0036211 / 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 ...: / : / protein modification process => GO:0036211 / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / 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 / 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 / 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 / CDK-mediated phosphorylation and removal of Cdc6 / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Ryabov, Y. / Fushman, D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. Authors: Ryabov, Y. / Fushman, D. #1: Journal: J.Am.Chem.Soc. / Year: 2006 Title: An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation. Authors: Ryabov, Y. / Geraghty, C. / Varshney, A. / Fushman, D. #2: Journal: J.Am.Chem.Soc. / Year: 2007 Title: A Model of Interdomain Mobility in a Multidomain Protein Authors: Ryabov, Y. / Fushman, D. #3: Journal: J.Mol.Biol. / Year: 2002 Title: Structural Properties of Polyubiquitin Chains in Solution Authors: Varadan, R. / Walker, O. / Picart, C. / Fushman, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pe9.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pe9.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pe9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pe9_validation.pdf.gz | 245.4 KB | Display | wwPDB validaton report |
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Full document | 2pe9_full_validation.pdf.gz | 245.2 KB | Display | |
Data in XML | 2pe9_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 2pe9_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/2pe9 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/2pe9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: DI-UBIQUITIN, 90% WATER/10% D20 |
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Sample conditions | Ionic strength: 20mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 298.0 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Software ordinal: 1 Details: THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI- UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL ...Details: THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI- UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL UBIQUITIN DOMAINS WITHIN THE MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS. FOR EACH UBIQUITIN DOMAIN THE STRUCTURE OF THE FIRST CONFORMER OF PDB ENTRY 1D3Z WAS ASSUMED. THE DEPOSITED CONFORMATION REPRESENTS ONE OF THE TWO EXPERIMENTALLY DETECTABLE CONFORMATIONS OF DI-UBIQUITIN AT PH 6.8. THE OCCUPATION PROBABILITY OF THIS CONFORMATION IS APPROXIMATELY 10%. CHAIN A CORRESPONDS TO UBIQUITIN DOMAIN THAT HAS A FREE C-TERMINUS IN DI-UBIQUITIN. CHAIN B CORRESPONDS TO UBIQUITIN DOMAIN THAT IN DI-UBIQUITIN IS LINKED VIA AN ISOPEPTIDE BOND BETWEEN ITS C- TERMINAL GLY76 AND LYS48 OF CHAIN A. THE ISOPEPTIDE BOND WAS PRESENT IN THE DI-UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER, BECAUSE THIS STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION AND TRANSLATION AND NO CONSTRAINTS REPRESENTING THE INTERDOMAIN LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE IS NOT PRESENT IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH UBIQUTIN DOMAINS (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR DATA ANALYSIS AND THEREFORE ARE NOT PRESENT IN THIS STRUCTURE. | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers submitted total number: 1 |