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- PDB-3k66: X-ray crystal structure of the E2 domain of C. elegans APL-1 -

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Basic information

Entry
Database: PDB / ID: 3k66
TitleX-ray crystal structure of the E2 domain of C. elegans APL-1
ComponentsBeta-amyloid-like protein
KeywordsCELL ADHESION / X-ray crystal structure / amyloid precursor protein / heparin binding / Alternative splicing / Amyloid / Developmental protein / Differentiation / Glycoprotein / Membrane / Neurogenesis / Transmembrane
Function / homology
Function and homology information


ecdysis, collagen and cuticulin-based cuticle / G alpha (q) signalling events / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / ECM proteoglycans / Platelet degranulation / body morphogenesis / nematode larval development / transition metal ion binding ...ecdysis, collagen and cuticulin-based cuticle / G alpha (q) signalling events / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / ECM proteoglycans / Platelet degranulation / body morphogenesis / nematode larval development / transition metal ion binding / axonogenesis / central nervous system development / heparin binding / cytoplasmic vesicle / early endosome / neuron projection / neuronal cell body / membrane
Similarity search - Function
Amyloid precursor protein, E2 domain / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. ...Amyloid precursor protein, E2 domain / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Amyloid-beta-like protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.7 Å
AuthorsHoopes, J.T. / Ha, Y.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Structural characterization of the E2 domain of APL-1, a Caenorhabditis elegans homolog of human amyloid precursor protein, and its heparin binding site
Authors: Hoopes, J.T. / Liu, X. / Xu, X. / Demeler, B. / Folta-Stogniew, E. / Li, C. / Ha, Y.
#1: Journal: Mol.Cell / Year: 2004
Title: The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain.
Authors: Wang, Y. / Ha, Y.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-amyloid-like protein


Theoretical massNumber of molelcules
Total (without water)28,5161
Polymers28,5161
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.621, 97.621, 67.975
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-amyloid-like protein


Mass: 28516.445 Da / Num. of mol.: 1 / Fragment: E2 Domain: UNP residues 240-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: apl-1, C42D8.8 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10651
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 15% Isopropanol, 0.1 M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 15, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 10475 / Redundancy: 9.7 % / Rsym value: 0.055 / Net I/σ(I): 25.4

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Processing

Software
NameClassification
CrystalCleardata collection
HKL2Mapmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→30 Å / σ(F): 2
RfactorNum. reflection
Rfree0.299 -
Rwork0.251 -
obs0.251 10475
Displacement parametersBiso mean: 73.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 75 1796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.28
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 10

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