[English] 日本語
Yorodumi- PDB-1c3t: ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3t | ||||||
---|---|---|---|---|---|---|---|
Title | ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY | ||||||
Components | PROTEIN (1D8 UBIQUITIN) | ||||||
Keywords | DE NOVO PROTEIN / PROTEIN DESIGN / HYDROPHOBIC CORE / PACKING / ROTAMERS / ROC / UBIQUITIN | ||||||
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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / 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 / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / 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 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / 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 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / 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 / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL., J MOL BIOL, 1997, 269: 408- 422), EXPLICIT SWAPPING OF NON- STEREOSPECIFICALLY ASSIGNED METHYLS, METHYLENES (FOLMER ET AL. J BIOMOL NMR, 1997, 9: 245-258). | ||||||
Authors | Lazar, G.A. / Johnson, E.C. / Desjarlais, J.R. / Handel, T.M. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Rotamer strain as a determinant of protein structural specificity. Authors: Lazar, G.A. / Johnson, E.C. / Desjarlais, J.R. / Handel, T.M. #1: Journal: Protein Sci. / Year: 1997 Title: De Novo Design of the Hydrophobic Core of Ubiquitin Authors: Lazar, G.A. / Desjarlais, J.R. / Handel, T.M. #2: Journal: Structure Fold.Des. / Year: 1999 Title: Solution Structure and Dynamics of a Designed Hydrophobic Core Variant of Ubiquitin Authors: Johnson, E.C. / Lazar, G.A. / Desjarlais, J.R. / Handel, T.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c3t.cif.gz | 479.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c3t.ent.gz | 399.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3t ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3t | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8576.831 Da / Num. of mol.: 1 / Mutation: I3L,I13L,L15V,V17L,I23V,V26L,I61L,L67I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62988, UniProt: P0CG48*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||
NMR details | Text: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY. |
-Sample preparation
Details | Contents: 2 MM 13C/15N 1D8 UBIQUITIN, 25 MM SODIUM PHOSPHATE, 25 MM SODIUM ACETATE (D3), 0.02% SODIUM AZIDE, PH 5.8 |
---|---|
Sample conditions | Ionic strength: 50 mM / pH: 5.80 / Pressure: 1 atm / Temperature: 303.00 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
---|
-Processing
Refinement | Method: RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL., J MOL BIOL, 1997, 269: 408- 422), EXPLICIT SWAPPING OF NON- STEREOSPECIFICALLY ASSIGNED ...Method: RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL., J MOL BIOL, 1997, 269: 408- 422), EXPLICIT SWAPPING OF NON- STEREOSPECIFICALLY ASSIGNED METHYLS, METHYLENES (FOLMER ET AL. J BIOMOL NMR, 1997, 9: 245-258). Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING 3212 NONREDUNDANT NOE RESTRAINTS, 84 DIHEDRAL RESTRAINTS, AND 68 H-BOND RESTRAINTS. |
---|---|
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 20 |