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- PDB-3dbl: Structural Dissection of a Gating Mechanism Preventing Misactivat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dbl | ||||||
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Title | Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) | ||||||
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![]() | CELL CYCLE / activating enzyme / Apoptosis / Membrane / Ubl conjugation pathway / ATP-binding / Ligase / Nucleotide-binding / Polymorphism / Nucleus | ||||||
Function / homology | ![]() E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / regulation of proteolysis / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis ...E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / regulation of proteolysis / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / regulation of neuron apoptotic process / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Iron uptake and transport / protein modification process / protein localization / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / Antigen processing: Ubiquitination & Proteasome degradation / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / neuron apoptotic process / regulation of cell cycle / protein ubiquitination / protein heterodimerization activity / ubiquitin protein ligase binding / DNA damage response / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / proteolysis / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
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Method | ![]() ![]() | ||||||
![]() | Souphron, J. / Schulman, B.A. | ||||||
![]() | ![]() Title: Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1. Authors: Souphron, J. / Waddell, M.B. / Paydar, A. / Tokgoz-Gromley, Z. / Roussel, M.F. / Schulman, B.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 798.6 KB | Display | ![]() |
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PDB format | ![]() | 650.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 561.3 KB | Display | ![]() |
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Full document | ![]() | 725.8 KB | Display | |
Data in XML | ![]() | 151.7 KB | Display | |
Data in CIF | ![]() | 203.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dbhSC ![]() 3dbrC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59973.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 48767.750 Da / Num. of mol.: 4 / Mutation: C216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8TBC4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #3: Protein | Mass: 9692.143 Da / Num. of mol.: 4 / Mutation: A172Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 117851 / Num. obs: 116696 / % possible obs: 93.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.8 / Num. unique all: 9776 / % possible all: 78.6 |
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Processing
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB entry 3DBH Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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