[English] 日本語
Yorodumi
- PDB-5kk3: Atomic Resolution Structure of Monomorphic AB42 Amyloid Fibrils -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kk3
TitleAtomic Resolution Structure of Monomorphic AB42 Amyloid Fibrils
ComponentsBeta-amyloid protein 42
KeywordsPROTEIN FIBRIL / amyloid beta / fibril
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 synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / 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 / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / 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 / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / 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 / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / 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)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

#1: Protein/peptide
Beta-amyloid protein 42 / 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

-
Experimental details

-
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

-
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 / Pressure: 1 atm / Temperature: 277 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more