+Open data
-Basic information
Entry | Database: PDB / ID: 6bh8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ZMPSTE24 in complex with phosphoramidon | ||||||
Components | CAAX prenyl protease 1 homolog | ||||||
Keywords | HYDROLASE / Integral Membrane Protein / Zinc Metalloprotease / Inhibitor Complex | ||||||
Function / homology | Function and homology information prenylated protein catabolic process / regulation of stress-activated protein kinase signaling cascade / regulation of mitotic cell cycle DNA replication / regulation of termination of RNA polymerase I transcription / Ste24 endopeptidase / CAAX-box protein processing / positive regulation of gene expression via chromosomal CpG island demethylation / inflammatory cell apoptotic process / regulation of hormone metabolic process / response to DNA damage checkpoint signaling ...prenylated protein catabolic process / regulation of stress-activated protein kinase signaling cascade / regulation of mitotic cell cycle DNA replication / regulation of termination of RNA polymerase I transcription / Ste24 endopeptidase / CAAX-box protein processing / positive regulation of gene expression via chromosomal CpG island demethylation / inflammatory cell apoptotic process / regulation of hormone metabolic process / response to DNA damage checkpoint signaling / kidney morphogenesis / cellular lipid metabolic process / cardiac ventricle development / maintenance of rDNA / nuclear envelope organization / growth plate cartilage development / ventricular cardiac muscle tissue development / regulation of fibroblast proliferation / calcium ion import into sarcoplasmic reticulum / regulation of cellular senescence / regulation of TOR signaling / CAMKK-AMPK signaling cascade / cardiac conduction / regulation of defense response to virus / metalloexopeptidase activity / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / adult walking behavior / : / negative regulation of miRNA processing / cardiac muscle cell development / nuclear inner membrane / regulation of DNA damage response, signal transduction by p53 class mediator / neuromuscular process / bone mineralization / regulation of lipid metabolic process / regulation of multicellular organism growth / regulation of glucose metabolic process / hair follicle development / heart morphogenesis / thymus development / liver development / regulation of autophagy / determination of adult lifespan / multicellular organism growth / cellular response to gamma radiation / metalloendopeptidase activity / late endosome membrane / regulation of cell shape / double-stranded DNA binding / early endosome membrane / DNA repair / endoplasmic reticulum membrane / protein-containing complex / proteolysis / extracellular exosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å | ||||||
Authors | Goblirsch, B.R. / Arachea, B.T. / Wiener, M.C. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Phosphoramidon inhibits the integral membrane protein zinc metalloprotease ZMPSTE24. Authors: Goblirsch, B.R. / Arachea, B.T. / Councell, D.J. / Wiener, M.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6bh8.cif.gz | 313.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6bh8.ent.gz | 257 KB | Display | PDB format |
PDBx/mmJSON format | 6bh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/6bh8 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/6bh8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5sytS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55714.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZMPSTE24, FACE1, STE24 / Plasmid: pSGP47 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: O75844, Ste24 endopeptidase #2: Chemical | #3: Chemical | #4: Chemical | Sequence details | The deposited sequence is derived from NCBI GenBank entry BC037283.1 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.64 Å3/Da / Density % sol: 73.48 % / Description: Long needle-like morphology |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Glycerol, Ammonium Sulfate, PEG 3350, Hepes/NaOH pH 7.5 Temp details: Crystallization set-ups at 296 and then immediately moved to 277 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2017 |
Radiation | Monochromator: Double crystal Monochromator, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.85→47.03 Å / Num. obs: 19383 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 111.68 Å2 / CC1/2: 0.761 / Rmerge(I) obs: 0.5105 / Rpim(I) all: 0.3347 / Rrim(I) all: 0.6127 / Net I/σ(I): 2.21 |
Reflection shell | Resolution: 3.85→3.99 Å / Redundancy: 3.3 % / Rmerge(I) obs: 2.291 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 187 / CC1/2: 0.326 / Rpim(I) all: 1.468 / Rrim(I) all: 2.729 / % possible all: 97.38 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5SYT Resolution: 3.85→47.028 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.21
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 373.37 Å2 / Biso mean: 143.7474 Å2 / Biso min: 10.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.85→47.028 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|