+Open data
-Basic information
Entry | Database: PDB / ID: 3tpl | ||||||
---|---|---|---|---|---|---|---|
Title | APO Structure of BACE1 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / MEMAPSIN 2 / PROTEASE / Beta-secretase 1 | ||||||
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: 2.5 Å | ||||||
Authors | Xu, Y.C. / Li, M.J. / Greenblatt, H. / Chen, T.T. / Silman, I. / Sussman, J.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations Authors: Xu, Y.C. / Li, M.J. / Greenblatt, H. / Chen, W.Y. / Paz, A. / Dym, O. / Peleg, Y. / Chen, T.T. / Shen, X. / He, J.H. / Jiang, H.L. / Silman, I. / Sussman, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tpl.cif.gz | 226.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tpl.ent.gz | 178.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tpl_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tpl_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | 3tpl_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 3tpl_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/3tpl ftp://data.pdbj.org/pub/pdb/validation_reports/tp/3tpl | HTTPS FTP |
-Related structure data
Related structure data | 3tpjC 3tppC 3tprC 2b8lS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48222.922 Da / Num. of mol.: 3 / Fragment: UNP residues 43-454 / Mutation: K75A, E77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 20-25%(w/v)PEG 5000, 200mM monomethyl ether, 200mM ammonium iodide, 200mM sodium citrate, pH 6.4, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
---|---|
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.7 Å / Num. obs: 54129 / Observed criterion σ(I): 4.64 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B8L Resolution: 2.5→46.755 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.42 / σ(F): 1.99 / Phase error: 29.96 / Stereochemistry target values: MLHL
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.183 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.68 Å2 / Biso mean: 55.9971 Å2 / Biso min: 30.55 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.755 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
|