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- PDB-2fk3: Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copp... -

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Basic information

Entry
Database: PDB / ID: 2fk3
TitleStructure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'large unit cell' form
ComponentsAmyloid beta A4 protein precursor
KeywordsMETAL BINDING PROTEIN / Alpha-Beta Two-layered Sandwich / Non-Crystallographic Symmetry
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 / Lysosome Vesicle Biogenesis / astrocyte projection / 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 / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / main axon / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / 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 / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / 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 / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / 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
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, 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKong, G.K.-W. / Parker, M.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Studies of the Alzheimer's Amyloid Precursor Protein Copper-binding Domain Reveal How it Binds Copper Ions
Authors: Kong, G.K. / Adams, J.J. / Harris, H.H. / Boas, J.F. / Curtain, C.C. / Galatis, D. / Masters, C.L. / Barnham, K.J. / McKinstry, W.J. / Cappai, R. / Parker, M.W.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_biol / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 precursor
B: Amyloid beta A4 protein precursor
C: Amyloid beta A4 protein precursor
D: Amyloid beta A4 protein precursor
E: Amyloid beta A4 protein precursor
F: Amyloid beta A4 protein precursor
G: Amyloid beta A4 protein precursor
H: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,99927
Polymers54,7918
Non-polymers1,20719
Water3,405189
1
A: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1035
Polymers6,8491
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9763
Polymers6,8491
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0404
Polymers6,8491
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9763
Polymers6,8491
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0404
Polymers6,8491
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0404
Polymers6,8491
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Amyloid beta A4 protein precursor


Theoretical massNumber of molelcules
Total (without water)6,8491
Polymers6,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Amyloid beta A4 protein precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9763
Polymers6,8491
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.623, 67.437, 127.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Amyloid beta A4 protein precursor


Mass: 6848.926 Da / Num. of mol.: 8 / Fragment: Residues 133 to 189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP / Plasmid: pPIC-9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P05067
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1 M MES pH 5.4 - 5.6, 0.4 M NaCOOH, 10 - 15 % (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.3786 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 2003 / Details: Bent cylindrical Si-mirror (Rh coated)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3786 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 20578 / Num. obs: 20981 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 11.4 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.072 / Net I/σ(I): 30.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 9.3 / Rsym value: 0.143 / % possible all: 86.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1444276.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1047 5.1 %RANDOM
Rwork0.208 ---
obs0.208 20355 98.1 %-
all-21402 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.6865 Å2 / ksol: 0.369541 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--2.39 Å20 Å2
3----3.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 19 189 3990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 159 5.3 %
Rwork0.246 2843 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_ed.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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