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Yorodumi- PDB-3fn1: E2-RING expansion of the NEDD8 cascade confers specificity to cul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fn1 | ||||||
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Title | E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification. | ||||||
Components |
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Keywords | LIGASE / ATP-binding / Cell cycle / Nucleotide-binding / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / NEDD8 ligase activity / post-translational protein modification / NIK-->noncanonical NF-kB signaling ...NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / NEDD8 ligase activity / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of cell cycle / protein heterodimerization activity / protein-containing complex / proteolysis / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Huang, D.T. / Ayrault, O. / Hunt, H.W. / Taherbhoy, A.M. / Duda, D.M. / Scott, D.C. / Borg, L.A. / Neale, G. / Murray, P.J. / Roussel, M.F. / Schulman, B.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification Authors: Huang, D.T. / Ayrault, O. / Hunt, H.W. / Taherbhoy, A.M. / Duda, D.M. / Scott, D.C. / Borg, L.A. / Neale, G. / Murray, P.J. / Roussel, M.F. / Schulman, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fn1.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fn1.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/3fn1 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/3fn1 | HTTPS FTP |
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-Related structure data
Related structure data | 1y8xS 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: 10856.974 Da / Num. of mol.: 1 / Fragment: UBIQUITIN-ACTIVATING ENZYME E1C, residue 368-463 / Mutation: L394M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: E1C, UBA3, UBE1C / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q8TBC4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein | Mass: 19104.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCE2, UBE2F / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q969M7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#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: 3.38 Å3/Da / Density % sol: 63.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.7-0.8 M Na Citrate, 0.2 M NaC1, 0.1 M Bicine, 5 mM DTT, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 15203 / Num. obs: 13512 / % possible obs: 96.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.13 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Y8X Resolution: 2.5→24.88 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.26 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.41 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→24.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -16.5251 Å / Origin y: 5.2531 Å / Origin z: 12.9471 Å
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Refinement TLS group |
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