+Open data
-Basic information
Entry | Database: PDB / ID: 2zhu | ||||||
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Title | Crystal structure of BACE1 at pH 5.0 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / pH 5.0 / Alternative splicing / Aspartyl protease / Glycoprotein / Membrane / Protease / Transmembrane / Zymogen | ||||||
Function / homology | Function and homology information memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / protein processing / recycling endosome / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shimizu, H. / Nukina, N. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2008 Title: Crystal structure of an active form of BACE1, an enzyme responsible for amyloid beta protein production Authors: Shimizu, H. / Tosaki, A. / Kaneko, K. / Hisano, T. / Sakurai, T. / Nukina, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zhu.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zhu.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zhu_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 2zhu_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 2zhu_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2zhu_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/2zhu ftp://data.pdbj.org/pub/pdb/validation_reports/zh/2zhu | HTTPS FTP |
-Related structure data
Related structure data | 2zhrC 2zhsC 2zhtC 2zhvSC 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: 45900.500 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 45-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1 / Plasmid: pet11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56817, memapsin 2 |
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#2: 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: 2.87 Å3/Da / Density % sol: 57.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 22% PEG 5000 MME, 0.2M Sodium Acetate pH 6.5, 0.2M Ammonium Iodide, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 21653 / % possible obs: 99.1 % / Redundancy: 4.5 % / Rsym value: 0.069 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2117 / Rsym value: 0.388 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZHV Resolution: 2.4→49.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2370418.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.3763 Å2 / ksol: 0.353871 e/Å3 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.31 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.4 Å / Total num. of bins used: 6 /
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Xplor file |
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