+Open data
-Basic information
Entry | Database: PDB / ID: 5k1c | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the UAF1/WDR20/USP12 complex | ||||||
Components |
| ||||||
Keywords | HYDROLASE / WD40 repeat domain / WDR20 / USP12 / UAF1 / WDR48 / deubiquitinating enzyme / Ubiquitin-specific protease / USP1-associated factor 1 | ||||||
Function / homology | Function and homology information regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / protein deubiquitination / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization / embryonic organ development / ubiquitin binding / positive regulation of epithelial cell proliferation / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of receptor signaling pathway via JAK-STAT / double-strand break repair via homologous recombination / multicellular organism growth / late endosome / single-stranded DNA binding / spermatogenesis / double-stranded DNA binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / DNA damage response / proteolysis / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Li, H. / D'Andrea, A.D. / Zheng, N. | ||||||
Citation | Journal: Mol.Cell / Year: 2016 Title: Allosteric Activation of Ubiquitin-Specific Proteases by beta-Propeller Proteins UAF1 and WDR20. Authors: Li, H. / Lim, K.S. / Kim, H. / Hinds, T.R. / Jo, U. / Mao, H. / Weller, C.E. / Sun, J. / Chatterjee, C. / D'Andrea, A.D. / Zheng, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5k1c.cif.gz | 259.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5k1c.ent.gz | 202.9 KB | Display | PDB format |
PDBx/mmJSON format | 5k1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k1c_validation.pdf.gz | 477.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5k1c_full_validation.pdf.gz | 493.9 KB | Display | |
Data in XML | 5k1c_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 5k1c_validation.cif.gz | 62.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/5k1c ftp://data.pdbj.org/pub/pdb/validation_reports/k1/5k1c | HTTPS FTP |
-Related structure data
Related structure data | 5k16SC 5k19SC 5k1aSC 5k1bC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41256.684 Da / Num. of mol.: 1 / Fragment: residues 16-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP12, UBH1, USP12L1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: O75317, ubiquitinyl hydrolase 1 |
---|
-WD repeat-containing protein ... , 2 types, 2 molecules BC
#2: Protein | Mass: 63224.582 Da / Num. of mol.: 1 / Fragment: residues 1-563 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q8TAF3 |
---|---|
#3: Protein | Mass: 62977.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR20 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8TBZ3 |
-Non-polymers , 4 types, 78 molecules
#4: Chemical | ChemComp-ZN / |
---|---|
#5: Chemical | ChemComp-PO4 / |
#6: Chemical | ChemComp-TAM / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 73.14 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M MES, 1.3 M ammonium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50.01 Å / Num. obs: 58534 / % possible obs: 97.8 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.109 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.5 / % possible all: 98.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K16, 5K19 and 5K1A Resolution: 3→50.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.881 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|