+Open data
-Basic information
Entry | Database: PDB / ID: 5m3n | ||||||
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Title | HTRA2 wild-type structure | ||||||
Components | Serine protease HTRA2, mitochondrial | ||||||
Keywords | HYDROLASE / Serine Protease Parkinson Disease Mitochondria PDZ domain Dynamics | ||||||
Function / homology | Function and homology information HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / ceramide metabolic process / regulation of autophagy of mitochondrion / mitochondrial protein catabolic process / CD40 receptor complex / : / programmed cell death ...HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / ceramide metabolic process / regulation of autophagy of mitochondrion / mitochondrial protein catabolic process / CD40 receptor complex / : / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / serine-type endopeptidase complex / adult walking behavior / response to herbicide / positive regulation of protein targeting to mitochondrion / execution phase of apoptosis / positive regulation of execution phase of apoptosis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein autoprocessing / negative regulation of cell cycle / regulation of multicellular organism growth / neuron development / cellular response to interferon-beta / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to retinoic acid / forebrain development / Mitochondrial protein degradation / serine-type peptidase activity / mitochondrial membrane / protein catabolic process / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / cellular response to growth factor stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / unfolded protein binding / peptidase activity / cellular response to heat / cellular response to oxidative stress / neuron apoptotic process / negative regulation of neuron apoptotic process / cytoskeleton / positive regulation of apoptotic process / serine-type endopeptidase activity / chromatin / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / proteolysis / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å | ||||||
Authors | Merski, M. / Pereira, P.J.B. / Macedo-Ribeiro, S. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: Cell Death Dis / Year: 2017 Title: Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2. Authors: Merski, M. / Moreira, C. / Abreu, R.M. / Ramos, M.J. / Fernandes, P.A. / Martins, L.M. / Pereira, P.J.B. / Macedo-Ribeiro, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m3n.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3n.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m3n_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 5m3n_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 5m3n_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5m3n_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3n ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3n | HTTPS FTP |
-Related structure data
Related structure data | 5m3oC 5tnyC 5tnzC 5to0C 5to1C 1lcyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35977.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA2, OMI, PRSS25 / Production host: Escherichia coli (E. coli) / References: UniProt: O43464, HtrA2 peptidase |
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#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: Crystals were grown using the sitting drop vapor-diffusion method by mixing equal volumes of protein (10-15 mg/mL) and reservoir solution containing 0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→47.633 Å / Num. obs: 38703 / % possible obs: 98.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.65→1.74 Å / Num. measured obs: 38699 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LCY Resolution: 1.649→47.633 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.39 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.649→47.633 Å
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Refine LS restraints |
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LS refinement shell |
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