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- PDB-2y3j: Structure of segment AIIGLM from the amyloid-beta peptide (Ab, re... -

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Basic information

Entry
Database: PDB / ID: 2y3j
TitleStructure of segment AIIGLM from the amyloid-beta peptide (Ab, residues 30-35)
ComponentsAMYLOID BETA A4 PROTEIN
KeywordsPROTEIN FIBRIL / ALZHEIMER DISEASE
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / regulation of presynapse assembly / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / protein serine/threonine kinase binding / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / ionotropic glutamate receptor signaling pathway / response to interleukin-1 / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / dendritic shaft / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / visual learning / neuromuscular junction / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / 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 / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
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, 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 ...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 / 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: 1.99 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)4,9358
Polymers4,9358
Non-polymers00
Water362
1
A: AMYLOID BETA A4 PROTEIN
B: AMYLOID BETA A4 PROTEIN
C: AMYLOID BETA A4 PROTEIN
D: AMYLOID BETA A4 PROTEIN


Theoretical massNumber of molelcules
Total (without water)2,4674
Polymers2,4674
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-18.8 kcal/mol
Surface area2410 Å2
MethodPISA
2
E: AMYLOID BETA A4 PROTEIN
F: AMYLOID BETA A4 PROTEIN
G: AMYLOID BETA A4 PROTEIN
H: AMYLOID BETA A4 PROTEIN


Theoretical massNumber of molelcules
Total (without water)2,4674
Polymers2,4674
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-18.8 kcal/mol
Surface area2390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)9.560, 15.640, 45.230
Angle α, β, γ (deg.)89.87, 90.02, 89.91
Int Tables number1
Space group name H-MP1

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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: 616.814 Da / Num. of mol.: 8 / Fragment: RESIDUES 701-706 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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 30-AIIGLM-35 CORRESPONDS TO RESIDUES 701-706 OF APP

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.41 Å3/Da / Density % sol: 13.04 % / Description: NONE
Crystal growpH: 7
Details: AB3035 WAS DISSOLVED IN WATER AT 1MG/ML AND MIXED WITH 2 M SODIUM CHLORIDE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.875
11h,-k,-l20.012
11-h,-k,l30.051
11-H, K, -L40.062
ReflectionResolution: 2→45.23 Å / Num. obs: 1679 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 1.73 % / Biso Wilson estimate: 14.79 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.91
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.11 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→45.23 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.6 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 62 3.6 %RANDOM
Rwork0.22194 ---
obs0.22462 1679 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.107 Å2
Baniso -1Baniso -2Baniso -3
1-13.2 Å2-2.81 Å2-3.49 Å2
2---0.79 Å2-2.71 Å2
3----12.41 Å2
Refinement stepCycle: LAST / Resolution: 1.99→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms336 0 0 2 338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.712.135432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.574540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg28.4341572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1820.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02192
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: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.137 132 -
obs--88.59 %

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