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- PDB-5kk3: Atomic Resolution Structure of Monomorphic AB42 Amyloid Fibrils -

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Basic information

Entry
Database: PDB / ID: 5kk3
TitleAtomic Resolution Structure of Monomorphic AB42 Amyloid Fibrils
ComponentsBeta-amyloid protein 42Amyloid beta
KeywordsPROTEIN FIBRIL / amyloid beta / fibril
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / positive regulation of protein metabolic process / neuron projection maintenance / cholesterol metabolic process / extracellular matrix organization / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / synapse organization / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation
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. / 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 / 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)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsColvin, M.T. / Silvers, R. / Zhe Ni, Q. / Can, T.V. / Sergeyev, I. / Rosay, M. / Donovan, K.J. / Michael, B. / Wall, J. / Linse, S. / Griffin, R.G.
Funding support United States, Germany, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)EB-003151 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)EB-002026 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)EB-002804 United States
German Research Foundation (DFG)SI2105/1-1 Germany
Citation
Journal: J.Am.Chem.Soc. / Year: 2016
Title: Atomic Resolution Structure of Monomorphic A beta 42 Amyloid Fibrils.
Authors: Colvin, M.T. / Silvers, R. / Ni, Q.Z. / Can, T.V. / Sergeyev, I. / Rosay, M. / Donovan, K.J. / Michael, B. / Wall, J. / Linse, S. / Griffin, R.G.
#1: Journal: J. Am. Chem. Soc. / Year: 2015
Title: High resolution structural characterization of AB42 amyloid fibrils by magic angle spinning NMR.
Authors: Colvin, M.T. / Silvers, R. / Frohm, B. / Su, Y. / Linse, S. / Griffin, R.G.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-amyloid protein 42
B: Beta-amyloid protein 42
C: Beta-amyloid protein 42
D: Beta-amyloid protein 42
E: Beta-amyloid protein 42
F: Beta-amyloid protein 42
G: Beta-amyloid protein 42
H: Beta-amyloid protein 42
I: Beta-amyloid protein 42
J: Beta-amyloid protein 42
K: Beta-amyloid protein 42
L: Beta-amyloid protein 42
M: Beta-amyloid protein 42
N: Beta-amyloid protein 42
O: Beta-amyloid protein 42
P: Beta-amyloid protein 42
Q: Beta-amyloid protein 42
R: Beta-amyloid protein 42


Theoretical massNumber of molelcules
Total (without water)81,36218
Polymers81,36218
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area46980 Å2
ΔGint-270 kcal/mol
Surface area17840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -
Representative

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Components

#1: Protein/peptide
Beta-amyloid protein 42 / Amyloid beta / Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor ...Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 4520.087 Da / Num. of mol.: 18 / Fragment: residues 672-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05067

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic1PAR 5 ms mixing
123isotropic1PAR 10 ms mixing
133isotropic1PAR 20 ms mixing
143isotropic2PAIN 30 ms mixing
153isotropic1DARR 25 ms mixing
164isotropic1DARR 100 ms mixing
1104isotropic1PAR 20 ms mixing
193isotropic2FS-REDOR
184isotropic2FS-REDOR
175isotropic1ZF-TEDOR 6.4 ms mixing
1135isotropic1ZF-TEDOR 12 ms mixing
1125isotropic1DARR 100 ms mixing
1116isotropic2DARR 400 ms mixing
1163isotropic13D NCACX
1153isotropic23D NCOCX
1143isotropic23D CONCA

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid31 mg/uL [U-100% 13C; U-100% 15N] AB42-M01-42, 20 mM sodium phosphate, 0.2 mM EDTA, 0.02 % sodium azide, 100% H2O100% of monomers were labeled with [U-100% 13C; U-100% 15N]100% U-13C/15N AB42-M01-42100% H2O
solid41 mg/uL [U-30% 13C; U-30% 15N] AB42-M01-42, 20 mM sodium phosphate, 0.2 mM EDTA, 0.02 % sodium azide, 100% H2O30% of monomers were labeled with [U-100% 13C; U-100% 15N], 70% of monomers were natural abundance prior to fibrilization30% U-13C/15N AB42-M01-42100% H2O
solid51 mg/uL [1,6-13C-glucose, U-100% 15N] AB42-M01-42, 20 mM sodium phosphate, 0.2 mM EDTA, 0.02 % sodium azide, 100% H2O1,6-13C-glucose/U-15N AB42-M01-42100% H2O
solid61 mg/uL [2-13C-glycerol, U-100% 15N] AB42-M01-42, 20 mM sodium phosphate, 0.2 mM EDTA, 0.02 % sodium azide, 100% H2O50% of monomers were labeled with [U-100% 15N], 50% of monomers were labeled with 2-13C-glycerol prior to fibrilization2-13C-glycerol/U-15N AB42-M01-42100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 g/LAB42-M01-42[U-100% 13C; U-100% 15N]3
20 mMsodium phosphatenatural abundance3
0.2 mMEDTAnatural abundance3
0.02 %sodium azidenatural abundance3
1 g/LAB42-M01-42[U-30% 13C; U-30% 15N]4
20 mMsodium phosphatenatural abundance4
0.2 mMEDTAnatural abundance4
0.02 %sodium azidenatural abundance4
1 g/LAB42-M01-42[1,6-13C-glucose, U-100% 15N]5
20 mMsodium phosphatenatural abundance5
0.2 mMEDTAnatural abundance5
0.02 %sodium azidenatural abundance5
1 g/LAB42-M01-42[2-13C-glycerol, U-100% 15N]6
20 mMsodium phosphatenatural abundance6
0.2 mMEDTAnatural abundance6
0.02 %sodium azidenatural abundance6
Sample conditionsIonic strength: 1 mM / Label: NMR Buffer / pH: 8.0 / Pressure: 1 atm / Temperature: 277 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6003
Home-built RUBEN750Home-builtRUBEN7507502

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.113Goddardchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR ensembleConformers submitted total number: 10

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