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Yorodumi- PDB-2ypt: Crystal structure of the human nuclear membrane zinc metalloprote... -
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-Basic information
Entry | Database: PDB / ID: 2ypt | ||||||
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Title | Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / 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 / negative regulation of mesenchymal cell proliferation / cellular lipid metabolic process / DNA double-strand break attachment to nuclear envelope / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Breakdown of the nuclear lamina / cardiac ventricle development / maintenance of rDNA / Nuclear Envelope Breakdown / nuclear envelope organization / growth plate cartilage development / ventricular cardiac muscle tissue development / regulation of fibroblast proliferation / nuclear pore localization / calcium ion import into sarcoplasmic reticulum / protein localization to nuclear envelope / regulation of cellular senescence / lamin filament / nuclear lamina / regulation of TOR signaling / CAMKK-AMPK signaling cascade / cardiac conduction / XBP1(S) activates chaperone genes / regulation of defense response to virus / Initiation of Nuclear Envelope (NE) Reformation / metalloexopeptidase activity / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of protein localization to nucleus / adult walking behavior / : / negative regulation of miRNA processing / nuclear migration / cardiac muscle cell development / regulation of telomere maintenance / intermediate filament / muscle organ development / nuclear inner membrane / negative regulation of cardiac muscle hypertrophy in response to stress / regulation of DNA damage response, signal transduction by p53 class mediator / neuromuscular process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / bone mineralization / negative regulation of release of cytochrome c from mitochondria / regulation of lipid metabolic process / protein localization to nucleus / regulation of multicellular organism growth / regulation of glucose metabolic process / hair follicle development / heterochromatin formation / heart morphogenesis / regulation of cell migration / Meiotic synapsis / thymus development / liver development / regulation of autophagy / determination of adult lifespan / negative regulation of extrinsic apoptotic signaling pathway / multicellular organism growth / cellular response to gamma radiation / regulation of protein stability / protein localization / structural constituent of cytoskeleton / metalloendopeptidase activity / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / site of double-strand break / nuclear envelope / late endosome membrane / regulation of cell shape / cellular response to hypoxia / double-stranded DNA binding / early endosome membrane / nuclear membrane / nuclear speck / negative regulation of cell population proliferation / DNA repair / endoplasmic reticulum membrane / positive regulation of gene expression / perinuclear region of cytoplasm / structural molecule activity / protein-containing complex / proteolysis / extracellular exosome / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.8 Å | ||||||
Authors | Pike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Savitsky, P. / Cooper, C.D.O. / Chaikuad, A. / Goubin, S. / Shrestha, L. / Li, Q. ...Pike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Savitsky, P. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ypt.cif.gz | 648.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ypt.ent.gz | 557.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ypt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypt ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 55648.473 Da / Num. of mol.: 4 / Mutation: YES 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: Protein/peptide | Mass: 452.589 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02545 #3: Chemical | ChemComp-ZN / Sequence details | CATALYTIC MUTANT. PUTATIVE CATALYTIC RESIDUE GLU336 MUTATED TO ALANINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.55 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→38.5 Å / Num. obs: 26943 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 134.21 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.6 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.8→38.5 Å / Cor.coef. Fo:Fc: 0.8843 / Cor.coef. Fo:Fc free: 0.8837 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.687 Details: 4AW6 USED AS LSSR TARGET REST OF 0.1. AUTONCS AND TLS. ONE TLS GROUP PER ENZYME PEPTIDE COMPLEX EMPLOYED
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Displacement parameters | Biso mean: 173.48 Å2
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Refine analyze | Luzzati coordinate error obs: 1.324 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→38.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.94 Å / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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