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- PDB-3k6b: X-ray crystal structure of the E2 domain of APL-1 from C. elegans... -

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Basic information

Entry
Database: PDB / ID: 3k6b
TitleX-ray crystal structure of the E2 domain of APL-1 from C. elegans, in complex with sucrose octasulfate (SOS)
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


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 / ecdysis, collagen and cuticulin-based cuticle / Platelet degranulation / ECM proteoglycans / body morphogenesis / nematode larval development / transition metal ion binding ...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 / ecdysis, collagen and cuticulin-based cuticle / Platelet degranulation / ECM proteoglycans / 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
2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / Amyloid-beta-like protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 2.0Apr 22, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0172
Polymers28,5161
Non-polymers5001
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.314, 97.314, 67.462
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: Sugar ChemComp-GU4 / 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / 2,3,4,6-tetra-O-sulfonato-alpha-D-glucose / 2,3,4,6-tetra-O-sulfonato-D-glucose / 2,3,4,6-tetra-O-sulfonato-glucose


Type: D-saccharide, alpha linking / Mass: 500.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O18S4
IdentifierTypeProgram
DGlcp[2S,3S,4S,6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-sulfo-3-sulfo-4-sulfo-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-Glcp2SO33SO34SO36SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.23 Å3/Da / Density % sol: 61.96 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 9028 / Redundancy: 9.6 % / Rsym value: 0.053 / Net I/σ(I): 20.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.346

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K66

3k66


Resolution: 2.8→40 Å / σ(F): 2.6
RfactorNum. reflectionSelection details
Rfree0.309 -random
Rwork0.262 --
obs0.262 9028 -
Displacement parametersBiso mean: 84.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 28 34 1775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.46

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