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- PDB-3rtm: Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Aminoqu... -

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Basic information

Entry
Database: PDB / ID: 3rtm
TitleStructure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide
ComponentsBeta-secretase 1
KeywordsHydrolase/Hydrolase Inhibitor / ASPARTYL PROTEASE / Hydrolase-Hydrolase Inhibitor complex
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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion ...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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion / prepulse inhibition / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / multivesicular body / hippocampal mossy fiber to CA3 synapse / response to lead ion / trans-Golgi network / recycling endosome / protein processing / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / 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
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Chem-RTM / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsSickmier, E.A.
CitationJournal: J.Med.Chem. / Year: 2011
Title: From Fragment Screening to In Vivo Efficacy: Optimization of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1).
Authors: Cheng, Y. / Judd, T.C. / Bartberger, M.D. / Brown, J. / Chen, K. / Fremeau, R.T. / Hickman, D. / Hitchcock, S.A. / Jordan, B. / Li, V. / Lopez, P. / Louie, S.W. / Luo, Y. / Michelsen, K. / ...Authors: Cheng, Y. / Judd, T.C. / Bartberger, M.D. / Brown, J. / Chen, K. / Fremeau, R.T. / Hickman, D. / Hitchcock, S.A. / Jordan, B. / Li, V. / Lopez, P. / Louie, S.W. / Luo, Y. / Michelsen, K. / Nixey, T. / Powers, T.S. / Rattan, C. / Sickmier, E.A. / St Jean, D.J. / Wahl, R.C. / Wen, P.H. / Wood, S.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6997
Polymers45,8221
Non-polymers8766
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.875, 101.875, 169.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Beta-secretase 1 / Aspartyl protease 2 / ASP2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta- ...Aspartyl protease 2 / ASP2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Memapsin-2 / Membrane-associated aspartic protease 2


Mass: 45822.445 Da / Num. of mol.: 1 / Fragment: UNP residues 43-453 / Mutation: R14K, R15K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-RTM / 3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide


Mass: 311.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 20% (w/v) PEG 5000 monomethylethyl ether (MME), 200mM sodium citrate (pH 6.6) and 200mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDate: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 13736 / % possible obs: 98.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.082 / Χ2: 1.06 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.855.70.38713080.989197.5
2.85-2.967.30.31313541.1199.5
2.96-3.180.23213451.097199.6
3.1-3.2680.18413621.081199.3
3.26-3.468.10.1413521.058199
3.46-3.7380.09713711.018199.1
3.73-4.17.90.0813711.038198.7
4.1-4.697.80.06713881.075198.3
4.69-5.887.50.05713941.102197.9
5.88-207.50.05614911.027196.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.2884 / WRfactor Rwork: 0.2169 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7863 / SU B: 14.563 / SU ML: 0.3 / SU R Cruickshank DPI: 1.1049 / SU Rfree: 0.3921 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 680 5 %RANDOM
Rwork0.2212 ---
obs0.2246 13653 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.55 Å2 / Biso mean: 54.768 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.73 Å20 Å2
2--1.45 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 38 54 3002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223022
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9554103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71423.723137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43515477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0391517
X-RAY DIFFRACTIONr_chiral_restr0.090.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212308
X-RAY DIFFRACTIONr_mcbond_it0.7511.51828
X-RAY DIFFRACTIONr_mcangle_it1.39922956
X-RAY DIFFRACTIONr_scbond_it1.66731194
X-RAY DIFFRACTIONr_scangle_it2.8514.51147
LS refinement shellResolution: 2.76→2.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 38 -
Rwork0.278 888 -
all-926 -
obs--93.91 %

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