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Yorodumi- PDB-2kn5: A Correspondence Between Solution-State Dynamics of an Individual... -
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-Basic information
Entry | Database: PDB / ID: 2kn5 | ||||||
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Title | A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family | ||||||
Components | Ubiquitin | ||||||
Keywords | GENE REGULATION / Backrub / Residual Dipolar Coupling / Backbone flexibility / Protein dynamics / Cytoplasm / Isopeptide bond / Nucleus / Phosphoprotein / Ubl conjugation | ||||||
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) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NF-kB is activated and signals survival / Regulation of PTEN localization / 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 / cytosolic ribosome / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Defective CFTR causes cystic fibrosis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Monte Carlo optimization of ensemble members | ||||||
Authors | Friedland, G.D. | ||||||
Citation | Journal: PLOS COMPUT.BIOL. / Year: 2009 Title: A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. Authors: Friedland, G.D. / Lakomek, N.A. / Griesinger, C. / Meiler, J. / Kortemme, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kn5.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kn5.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2kn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/2kn5 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/2kn5 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: This ensemble provides a model of the structural variation present in the structured regions of ubiquitin from residual dipolar coupling measurements in 23 alignment media. | ||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Monte Carlo optimization of ensemble members / Software ordinal: 1 Details: A 10,000-MEMBER SET OF STRUCTURES WAS GENERATED USING ROSETTA AND BACKRUB CONFORMATIONAL SAMPLING. THE 50-MEMBER ENSEMBLE PRESENTED HERE WAS OPTIMIZED BY SELECTING STRUCTURES FROM THIS SET ...Details: A 10,000-MEMBER SET OF STRUCTURES WAS GENERATED USING ROSETTA AND BACKRUB CONFORMATIONAL SAMPLING. THE 50-MEMBER ENSEMBLE PRESENTED HERE WAS OPTIMIZED BY SELECTING STRUCTURES FROM THIS SET THAT MAXIMIZE AGREEMENT WITH THE RESIDUAL DIPOLAR COUPLINGS. SEVERAL OF THE STRUCTURES IN ENSEMBLE ARE IDENTICAL AS CHOSEN BY THE OPTIMIZATION ALGORITHM. | |||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 50 / Conformers submitted total number: 50 |