+Open data
-Basic information
Entry | Database: PDB / ID: 5v89 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of DCN4 PONY domain bound to CUL1 WHB | ||||||
Components |
| ||||||
Keywords | Ligase / protein binding / E3 Ligase / Ligase - protein binding complex | ||||||
Function / homology | Function and homology information positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / ubiquitin conjugating enzyme binding / positive regulation of ubiquitin-protein transferase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex ...positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / ubiquitin conjugating enzyme binding / positive regulation of ubiquitin-protein transferase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / animal organ morphogenesis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / G1/S transition of mitotic cell cycle / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Guy, R.K. / Schulman, B.A. / Scott, D.C. / Hammill, J.T. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase. Authors: Scott, D.C. / Hammill, J.T. / Min, J. / Rhee, D.Y. / Connelly, M. / Sviderskiy, V.O. / Bhasin, D. / Chen, Y. / Ong, S.S. / Chai, S.C. / Goktug, A.N. / Huang, G. / Monda, J.K. / Low, J. / ...Authors: Scott, D.C. / Hammill, J.T. / Min, J. / Rhee, D.Y. / Connelly, M. / Sviderskiy, V.O. / Bhasin, D. / Chen, Y. / Ong, S.S. / Chai, S.C. / Goktug, A.N. / Huang, G. / Monda, J.K. / Low, J. / Kim, H.S. / Paulo, J.A. / Cannon, J.R. / Shelat, A.A. / Chen, T. / Kelsall, I.R. / Alpi, A.F. / Pagala, V. / Wang, X. / Peng, J. / Singh, B. / Harper, J.W. / Schulman, B.A. / Guy, R.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5v89.cif.gz | 172 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5v89.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 5v89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/5v89 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/5v89 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5v83C 5v86C 5v88C 3tduS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Monomer as determined by gel filtration |
-Components
#1: Protein | Mass: 22756.834 Da / Num. of mol.: 1 / Fragment: residues 102-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D4, KIAA0276 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92564 |
---|---|
#2: Protein | Mass: 9015.699 Da / Num. of mol.: 1 / Fragment: WHB subdomain residues 702-776 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13616 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % Description: The authors state that the density surrounding the CUL1WHB subdomain in this structure was relatively weak, presumably due to its lack of participation in forming crystal contacts. ...Description: The authors state that the density surrounding the CUL1WHB subdomain in this structure was relatively weak, presumably due to its lack of participation in forming crystal contacts. Therefore we modeled and built this chain largely from a previous high resolution and high quality structure of CUL1WHB, 3TDU. |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG3350, 0.2M LiSO4, 10mM TCEP, 10mM Bis-Tris Propane |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. obs: 36927 / % possible obs: 93.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Χ2: 1.061 / Net I/σ(I): 7.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TDU.pdb Resolution: 1.55→23.917 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.42
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.85 Å2 / Biso mean: 28.4826 Å2 / Biso min: 7.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→23.917 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
|