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- PDB-3ktm: Structure of the Heparin-induced E1-Dimer of the Amyloid Precurso... -

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Basic information

Entry
Database: PDB / ID: 3ktm
TitleStructure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)
ComponentsAmyloid beta A4 protein
KeywordsCELL ADHESION / SIGNALING PROTEIN / Protein Structure / Alzheimer disease / Amyloid / Amyloidosis / Apoptosis / Copper / Disease mutation / Disulfide bond / Endocytosis / Heparin-binding / Metal-binding / Neurodegeneration / Notch signaling pathway / Proteoglycan / Zinc
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / Lysosome Vesicle Biogenesis / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / main axon / transition metal ion binding / The NLRP3 inflammasome / regulation of multicellular organism growth / intracellular copper ion homeostasis / ECM proteoglycans / regulation of presynapse assembly / neuronal dense core vesicle / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / Mitochondrial protein degradation / axonogenesis / protein serine/threonine kinase binding / response to interleukin-1 / platelet alpha granule lumen / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / dendritic shaft / trans-Golgi network membrane / endosome lumen / positive regulation of long-term synaptic potentiation / adult locomotory behavior / positive regulation of interleukin-1 beta production / learning / Post-translational protein phosphorylation / positive regulation of JNK cascade / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nerve growth factor stimulus / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / recycling endosome / synapse organization / visual learning / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / neuron projection development / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane / G alpha (i) signalling events / perikaryon / G alpha (q) signalling events / dendritic spine
Similarity search - Function
Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / 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. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) ...Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / 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. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / 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 / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Dna Ligase; domain 1 / PH-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (3R)-butane-1,3-diol / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and biochemical analysis of the heparin-induced E1 dimer of the amyloid precursor protein.
Authors: Dahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E.
History
DepositionNov 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
G: Amyloid beta A4 protein
H: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,53425
Polymers174,0978
Non-polymers1,43717
Water5,080282
1
A: Amyloid beta A4 protein
C: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8606
Polymers43,5242
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid beta A4 protein
D: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9567
Polymers43,5242
Non-polymers4315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Amyloid beta A4 protein
H: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8606
Polymers43,5242
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Amyloid beta A4 protein
G: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8606
Polymers43,5242
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,7621
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
B: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
C: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
D: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9483
Polymers21,7621
Non-polymers1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
E: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
F: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,7621
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
G: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,7621
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
H: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.990, 143.990, 351.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Amyloid beta A4 protein / Alzheimer disease amyloid protein / ABPP / APP


Mass: 21762.080 Da / Num. of mol.: 8 / Fragment: UNP residues 18-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P05067
#2: Chemical
ChemComp-BU4 / (3R)-butane-1,3-diol


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.02 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.7→29 Å / Num. obs: 74422 / % possible obs: 99.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 69.152 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.85 Å / % possible obs: 99.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10822

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Processing

Software
NameClassification
MxCuBEdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWP, 2FJZ

1mwp

2fjz


Resolution: 2.7→29 Å
RfactorNum. reflection% reflection
Rfree0.2499 3735 5 %
Rwork0.2151 --
all-74570 -
obs-74407 99.8 %
Displacement parametersBiso mean: 48.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11065 0 89 282 11436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007975
X-RAY DIFFRACTIONc_angle_deg1.44886

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