+Open data
-Basic information
Entry | Database: PDB / ID: 5l6h | |||||||||
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Title | Uba1 in complex with Ub-ABPA3 covalent adduct | |||||||||
Components |
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Keywords | LIGASE / E1 enzyme / ubiquitin activation / Uba1 inhibitor / adenosyl sulfamate | |||||||||
Function / homology | Function and homology information Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ribosomal small subunit assembly / ubiquitin-dependent protein catabolic process / cytosolic small ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / DNA damage response / ubiquitin protein ligase binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Misra, M. / Schindelin, H. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Structure / Year: 2017 Title: Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme. Authors: Misra, M. / Kuhn, M. / Lobel, M. / An, H. / Statsyuk, A.V. / Sotriffer, C. / Schindelin, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l6h.cif.gz | 927.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l6h.ent.gz | 764.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l6h_validation.pdf.gz | 1009.1 KB | Display | wwPDB validaton report |
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Full document | 5l6h_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5l6h_validation.xml.gz | 90.4 KB | Display | |
Data in CIF | 5l6h_validation.cif.gz | 130 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/5l6h ftp://data.pdbj.org/pub/pdb/validation_reports/l6/5l6h | HTTPS FTP |
-Related structure data
Related structure data | 5l6iC 5l6jC 4nnjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 2 types, 5 molecules ACBDE
#1: Protein | Mass: 114409.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UBA1, YKL210W / Production host: Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme #2: Protein | Mass: 8568.769 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759 |
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-Non-polymers , 7 types, 1016 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 143279 / % possible obs: 99.5 % / Redundancy: 7.5 % / Rsym value: 0.107 / Net I/σ(I): 13.3 |
Reflection shell | Highest resolution: 2.3 Å / Rsym value: 1.866 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NNJ Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 14.453 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.126 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→20 Å
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Refine LS restraints |
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