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- PDB-2y3l: Structure of segment MVGGVVIA from the amyloid-beta peptide (Ab, ... -

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Basic information

Entry
Database: PDB / ID: 2y3l
TitleStructure of segment MVGGVVIA from the amyloid-beta peptide (Ab, residues 35-42), alternate polymorph 2
ComponentsAMYLOID BETA A4 PROTEIN
KeywordsPROTEIN FIBRIL / ALZHEIMER DISEASE
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / regulation of synapse structure or activity / positive regulation of synaptic transmission, cholinergic / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / peptidase activator activity / PTB domain binding / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / neuron remodeling / astrocyte projection / regulation of multicellular organism growth / nuclear envelope lumen / dendrite development / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / negative regulation of long-term synaptic potentiation / signaling receptor activator activity / Notch signaling pathway / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / intracellular copper ion homeostasis / modulation of excitatory postsynaptic potential / main axon / ECM proteoglycans / positive regulation of T cell migration / response to insulin-like growth factor stimulus / regulation of presynapse assembly / extracellular matrix organization / swimming behavior / adult locomotory behavior / neuronal dense core vesicle / regulation of long-term neuronal synaptic plasticity / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / positive regulation of chemokine production / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / neuron projection maintenance / clathrin-coated pit / visual learning / cellular response to cAMP / astrocyte activation / synaptic cleft / Mitochondrial protein degradation / response to interleukin-1 / platelet alpha granule lumen / regulation of neuron apoptotic process / positive regulation of glycolytic process / learning / ionotropic glutamate receptor signaling pathway / locomotory behavior / cellular response to copper ion / endosome lumen / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / serine-type endopeptidase inhibitor activity / Post-translational protein phosphorylation / dendritic shaft / trans-Golgi network membrane / endocytosis / microglial cell activation / cellular response to nerve growth factor stimulus / regulation of translation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of JNK cascade / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / Golgi lumen / recycling endosome / response to lead ion / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / calcium ion transport / positive regulation of inflammatory response / regulation of gene expression / positive regulation of tumor necrosis factor production
Similarity search - Function
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / 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 / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsColletier, J.P. / Laganowsky, A. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular Basis for Amyloid-{Beta} Polymorphism.
Authors: Colletier, J. / Laganowsky, A. / Landau, M. / Zhao, M. / Soriaga, A.B. / Goldschmidt, L. / Flot, D. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.
History
DepositionDec 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
G: AMYLOID BETA A4 PROTEIN


Theoretical massNumber of molelcules
Total (without water)2,9804
Polymers2,9804
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-19 kcal/mol
Surface area3220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.470, 47.590, 20.800
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
AMYLOID BETA A4 PROTEIN / AMYLOID BETA PEPTIDE / ABPP / APPI / APP / ALZHEIMER DISEASE AMYLOID PROTEIN / CEREBRAL VASCULAR ...AMYLOID BETA PEPTIDE / ABPP / APPI / APP / ALZHEIMER DISEASE AMYLOID PROTEIN / CEREBRAL VASCULAR AMYLOID PEPTIDE / CVAP / PREA4 / PROTEASE NEXIN-II / PN-II


Mass: 744.943 Da / Num. of mol.: 4 / Fragment: RESIDUES 706-713 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067
Sequence detailsAMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF THE AMYLOID PRECURSOR PROTEIN (APP). AB ...AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF THE AMYLOID PRECURSOR PROTEIN (APP). AB SEGMENT 35-MVGGVVIA-42 CORRESPONDS TO RESIDUES 706-713 OF APP

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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: 1.38 Å3/Da / Density % sol: 10.91 % / Description: NONE
Crystal growpH: 7.5
Details: AB3542 CRYSTALS (FIRST DISSOLVED IN WATER) WERE FOUND IN 1.5-YEAR-OLD TRAYS SET AT 0.5 MG/ML IN 0.1 M HEPES PH 7.5, 0.5 M MG FORMATE (CRYSTAL FORM II)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→23.8 Å / Num. obs: 896 / % possible obs: 88.9 % / Observed criterion σ(I): 1.5 / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 2.54
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.91 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.55 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→23.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.99 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.717 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24699 53 5.6 %RANDOM
Rwork0.20165 ---
obs0.20435 896 88.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.899 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.1 Å2
2---0.58 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms204 0 0 0 204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8962.03268
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.591528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0391532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1740.240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 3 -
Rwork0.222 65 -
obs--88.31 %

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