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Yorodumi- PDB-3q3f: Engineering Domain-Swapped Binding Interfaces by Mutually Exclusi... -
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-Basic information
Entry | Database: PDB / ID: 3q3f | ||||||
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Title | Engineering Domain-Swapped Binding Interfaces by Mutually Exclusive Folding: Insertion of Ubiquitin into position 103 of Barnase | ||||||
Components | Ribonuclease/Ubiquitin chimeric protein | ||||||
Keywords | HYDROLASE / PROTEIN BINDING / domain swap / oligomerization / ubiquitin insertion | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / 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 ...Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / 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 / RNA endonuclease activity / 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 / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Stabilization of p53 / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.169 Å | ||||||
Authors | Ha, J.-H. / Karchin, J.M. / Walker-Kopp, N. / Huang, L.-S. / Berry, E.A. / Loh, S.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Engineering domain-swapped binding interfaces by mutually exclusive folding. Authors: Ha, J.H. / Karchin, J.M. / Walker-Kopp, N. / Huang, L.S. / Berry, E.A. / Loh, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q3f.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q3f.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 3q3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q3f_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 3q3f_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 3q3f_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3q3f_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/3q3f ftp://data.pdbj.org/pub/pdb/validation_reports/q3/3q3f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21128.715 Da / Num. of mol.: 1 Fragment: UNP P00648 48-150 and 151-157, UNP P0CG48 residues 2-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria), (gene. exp.) Homo sapiens (human) Gene: Barnase / Production host: Escherichia coli (E. coli) / References: UniProt: P00648, UniProt: P0CG48 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 3.9 Å3/Da / Density % sol: 68.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 mM Tris (pH 8.0), 1 M (NH4)2SO4, 1.5% isopropanol (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. all: 17704 / Num. obs: 17704 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.66 Å2 / Rsym value: 0.151 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.97 / Num. unique all: 778 / Rsym value: 0.505 / % possible all: 90.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3-103 of chain A of 1A2P, 1UBQ Resolution: 2.169→37.659 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 21.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.027 Å2 / ksol: 0.393 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.169→37.659 Å
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Refine LS restraints |
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LS refinement shell |
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