[English] 日本語
Yorodumi- PDB-1tt5: Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction req... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tt5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8 | ||||||
Components |
| ||||||
Keywords | CELL CYCLE / LIGASE | ||||||
Function / homology | Function and homology information E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / post-translational protein modification / regulation of neuron apoptotic process / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / neuron apoptotic process / regulation of apoptotic process / regulation of cell cycle / protein ubiquitination / protein heterodimerization activity / DNA damage response / ubiquitin protein ligase binding / signal transduction / protein-containing complex / proteolysis / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Huang, D.T. / Miller, D.W. / Mathew, R. / Cassell, R. / Holton, J.M. / Roussel, M.F. / Schulman, B.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Authors: Huang, D.T. / Miller, D.W. / Mathew, R. / Cassell, R. / Holton, J.M. / Roussel, M.F. / Schulman, B.A. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE Residue B SER 608 and Residue B VAL 701 are not linked. Distance of C-N bond is 6.15. ...SEQUENCE Residue B SER 608 and Residue B VAL 701 are not linked. Distance of C-N bond is 6.15. Residue B THR 384 and Residue B ASN 601 are linked together. The residues 600-1008 of chains B and D were modelled as alanines due to poor electron density. The residue names were assigned arbitrarily as there are multiple possible sequences consistent with the density, and the connectivity is unclear. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tt5.cif.gz | 375.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tt5.ent.gz | 298.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tt5_validation.pdf.gz | 497.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1tt5_full_validation.pdf.gz | 592.5 KB | Display | |
Data in XML | 1tt5_validation.xml.gz | 78 KB | Display | |
Data in CIF | 1tt5_validation.cif.gz | 105.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/1tt5 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/1tt5 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59973.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 4502169, UniProt: Q13564*PLUS #2: Protein | Mass: 48799.812 Da / Num. of mol.: 2 / Fragment: residues 33-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 38045942, UniProt: Q8TBC4*PLUS #3: Protein/peptide | Mass: 2875.364 Da / Num. of mol.: 2 / Fragment: residues 1-26 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2M, UBC12 / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61081 #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.57 % |
---|
-Data collection
Diffraction |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||
Reflection | Resolution: 2.6→18 Å / Num. obs: 67222 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→18 Å
| ||||||||||||||||||||
Xplor file |
|