[English] 日本語
Yorodumi- PDB-4aw6: Crystal structure of the human nuclear membrane zinc metalloprote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aw6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) | ||||||
Components | CAAX PRENYL PROTEASE 1 HOMOLOG | ||||||
Keywords | HYDROLASE / M48 PEPTIDASE / INTEGRAL MEMBRANE PROTEIN / PRELAMIN A PROCESSING / AGEING / PROGERIA | ||||||
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 / ventricular cardiac muscle tissue development / nuclear envelope organization / growth plate cartilage 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 / SAD / Resolution: 3.4 Å | ||||||
Authors | Pike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Cooper, C.D.O. / Chaikuad, A. / Goubin, S. / Shrestha, L. / Li, Q. / Mukhopadhyay, S. ...Pike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Cooper, C.D.O. / Chaikuad, A. / Goubin, S. / Shrestha, L. / Li, Q. / Mukhopadhyay, S. / Yang, J. / Xia, X. / Shintre, C.A. / Barr, A.J. / Berridge, G. / Chalk, R. / Bray, J.E. / von Delft, F. / Bullock, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Burgess-Brown, N. / Carpenter, E.P. | ||||||
Citation | Journal: Science / Year: 2013 Title: The Structural Basis of Zmpste24-Dependent Laminopathies. Authors: Quigley, A. / Dong, Y.Y. / Pike, A.C.W. / Dong, L. / Shrestha, L. / Berridge, G. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.N. / Burgess- ...Authors: Quigley, A. / Dong, Y.Y. / Pike, A.C.W. / Dong, L. / Shrestha, L. / Berridge, G. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.N. / Burgess-Brown, N.A. / Carpenter, E.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4aw6.cif.gz | 667.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4aw6.ent.gz | 559.3 KB | Display | PDB format |
PDBx/mmJSON format | 4aw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/4aw6 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/4aw6 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
3 |
| ||||||||||||||||
4 |
| ||||||||||||||||
5 |
| ||||||||||||||||
6 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||
Details | DETERMINED OLIGOMERIC STATE BY PISA (DIMERIC) DOES NOT MATCH OBSERVATIONS FROM IN-SOLUTION STUDIES WHERE THE PROTEIN IS MONOMERIC AS DETERMINED BY SEC/MALLS ANALYSIS. IN ADDITION THE 'DIMER' INTERFACE SEEN IN THIS ENTRY IS NOT OBSERVED IN A SECOND CRYSTAL FORM SUGGESTING THAT IT IS A FEATURE OF CRYSTAL PACKING RATHER THAN A BONA FIDE DIMERIZATION SURFACE. |
-Components
#1: Protein | Mass: 55706.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-CT10HF-LIC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75844, Ste24 endopeptidase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PC1 / Sequence details | NATURAL VARIANT THR137ALA | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.21 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→39.45 Å / Num. obs: 37469 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 129.24 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.4→37.96 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.8802 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.497
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 131.61 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 1.021 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→37.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.4→3.49 Å / Total num. of bins used: 19
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
|