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- PDB-2m05: Structure of module 2 from the E1 domain of C. elegans APL-1 -

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Basic information

Entry
Database: PDB / ID: 2m05
TitleStructure of module 2 from the E1 domain of C. elegans APL-1
ComponentsBeta-amyloid-like protein
KeywordsUNKNOWN FUNCTION / Apl-1 / Amyloid Precursor Protein
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 / ECM proteoglycans / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / 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 / ECM proteoglycans / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / 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
Amyloidogenic glycoprotein, copper-binding 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, copper-binding 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 (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 A4 / Amyloidogenic glycoprotein / Dna Ligase; domain 1 / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Amyloid-beta-like protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsHinds, M.G. / Leong, S.
CitationJournal: Metallomics / Year: 2013
Title: Quantification of copper binding to amyloid precursor protein domain 2 and its Caenorhabditis elegans ortholog. Implications for biological function.
Authors: Leong, S.L. / Young, T.R. / Barnham, K.J. / Wedd, A.G. / Hinds, M.G. / Xiao, Z. / Cappai, R.
History
DepositionOct 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)7,4281
Polymers7,4281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Beta-amyloid-like protein


Mass: 7428.443 Da / Num. of mol.: 1 / Fragment: module 2 of E1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: apl-1, C42D8.8 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q10651

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D HN(CO)CA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D C(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11112D 1H-1H NOESY
11213D CBCA(CO)NH

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Sample preparation

DetailsContents: 0.5 mM APL-1, 0.5 mM [U-100% 15N] APL-1, 0.5 mM [U-100% 13C; U-100% 15N] APL-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAPL-1-11
0.5 mMAPL-1-2[U-100% 15N]1
0.5 mMAPL-1-3[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 10 / pH: 6.9 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker AGcollection
XEASYBartels et al.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1056 / NOE intraresidue total count: 402 / NOE long range total count: 322 / NOE medium range total count: 102 / NOE sequential total count: 230 / Protein phi angle constraints total count: 51 / Protein psi angle constraints total count: 51
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å
NMR ensemble rmsDistance rms dev: 0.024 Å / Distance rms dev error: 0.001 Å

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