+Open data
-Basic information
Entry | Database: PDB / ID: 1ogw | ||||||
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Title | Synthetic Ubiquitin with fluoro-Leu at 50 and 67 | ||||||
Components | UBIQUITIN | ||||||
Keywords | CELL CYCLE / CHROMOSOMAL PROTEIN | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / Negative regulation of FGFR4 signaling / Iron uptake and transport Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Alexeev, D. / Ramage, R. / Young, D.W. / Sawyer, L. | ||||||
Citation | Journal: Chembiochem / Year: 2003 Title: Synthesis, Structural and Biological Studies of Ubiquitin Mutants Containing (2S, 4S)-5-Fluoroleucine Residues Strategically Placed in the Hydrophobic Core Authors: Alexeev, D. / Barlow, P.N. / Bury, S.M. / Charrier, J.-D. / Cooper, A. / Hadfield, D. / Jamieson, C. / Kelly, S.M. / Layfield, R. / Mayer, R.J. / Mcsparran, H. / Price, N.C. / Ramage, R. / ...Authors: Alexeev, D. / Barlow, P.N. / Bury, S.M. / Charrier, J.-D. / Cooper, A. / Hadfield, D. / Jamieson, C. / Kelly, S.M. / Layfield, R. / Mayer, R.J. / Mcsparran, H. / Price, N.C. / Ramage, R. / Sawyer, L. / Starkmann, B.A. / Uhrin, D. / Willken, J. / Young, D.W. #1: Journal: Biochem.J. / Year: 1994 Title: Synthetic, Structural and Biological Studies of the Ubiquitin System Authors: Alexeev, D. / Bury, S.M. / Turner, M.A. / Ogunjobi, O.M. / Muir, T.W. / Ramage, R. / Sawyer, L. #2: Journal: Biochem.J. / Year: 1997 Title: Synthetic, Structural and Biological Studies of the Ubiquitin System: The Synthesis and Crystal Structu of an Analogue Containing Unnatural Amino Acids Authors: Love, S.G. / Muir, T.W. / Ramage, R. / Shaw, K.T. / Alexeev, D. / Sawyer, L. / Kelly, S.M. / Price, N.C. / Arnold, J.E. / Lee, M.P. / Mayer, R.J. #3: Journal: J Mol Biol / Year: 1987 Title: Structure of ubiquitin refined at 1.8 A resolution. Abstract: The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond ...The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.5 degrees, respectively. A total of 58 water molecules per molecule of ubiquitin are included in the final model. The last four residues in the molecule appear to have partial occupancy or large thermal motion. The overall structure of ubiquitin is extremely compact and tightly hydrogen-bonded; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ogw.cif.gz | 30.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogw.ent.gz | 20 KB | Display | PDB format |
PDBx/mmJSON format | 1ogw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ogw_validation.pdf.gz | 395.3 KB | Display | wwPDB validaton report |
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Full document | 1ogw_full_validation.pdf.gz | 397.1 KB | Display | |
Data in XML | 1ogw_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 1ogw_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogw ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogw | HTTPS FTP |
-Related structure data
Related structure data | 1ubiS S: Starting model for refinement |
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Similar 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: 8612.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-76 / Source method: isolated from a natural source / Details: LEF IS (4S)-5-FLUORO-L-LEUCINE / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P0CG48 |
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#2: Water | ChemComp-HOH / |
Compound details | LEU (50) AND LEU (67) ARE MODIFIED RESIDUES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 32.68 % |
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Crystal grow | pH: 5.6 Details: SEEDED FROM DROP CONTAINING CONTAINING 5 MUL 20MG/ML UBIQUITIN AND 5 MUL 30% PEG 4000 IN 50MM CACODYLATE-HCL PH 5.6. STORED IN 38% PEG 4000. |
Crystal grow | *PLUS Method: other / Details: Love, S.G., (1997) Biochem. J., 323, 727. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→6 Å / Num. obs: 13828 / % possible obs: 89.9 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.31→1.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 81.4 |
Reflection | *PLUS Num. obs: 14305 / Num. measured all: 157103 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UBI Resolution: 1.32→8 Å / Num. parameters: 2814 / Num. restraintsaints: 2521 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 3212 / Occupancy sum non hydrogen: 2736 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |