[English] 日本語
Yorodumi
- EMDB-8720: VGSNKGAIIGL from Amyloid Beta determined by MicroED -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8720
TitleVGSNKGAIIGL from Amyloid Beta determined by MicroED
Map dataVGSNKGAIIGL from Amyloid Beta
SampleFibrils of Amyloid Beta segment 24-34:
Amyloid beta A4 protein / ligand
Function / homologyRIP-mediated NFkB activation via ZBP1 / Beta-amyloid precursor protein C-terminal / The NLRP3 inflammasome / Amyloidogenic glycoprotein, copper-binding domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain superfamily / Amyloid beta A4 protein / ECM proteoglycans / Amyloidogenic glycoprotein, E2 domain / Proteinase inhibitor I2, Kunitz, conserved site ...RIP-mediated NFkB activation via ZBP1 / Beta-amyloid precursor protein C-terminal / The NLRP3 inflammasome / Amyloidogenic glycoprotein, copper-binding domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain superfamily / Amyloid beta A4 protein / ECM proteoglycans / Amyloidogenic glycoprotein, E2 domain / Proteinase inhibitor I2, Kunitz, conserved site / Amyloidogenic glycoprotein, intracellular domain, conserved site / Amyloidogenic glycoprotein, extracellular domain conserved site / Amyloidogenic glycoprotein, heparin-binding / Pancreatic trypsin inhibitor Kunitz domain superfamily / Amyloidogenic glycoprotein, amyloid-beta peptide / PH-like domain superfamily / G alpha (q) signalling events / G alpha (i) signalling events / Amyloidogenic glycoprotein, copper-binding / Lysosome Vesicle Biogenesis / Amyloidogenic glycoprotein / Amyloidogenic glycoprotein, extracellular / Pancreatic trypsin inhibitor Kunitz domain / Formyl peptide receptors bind formyl peptides and many other ligands / Advanced glycosylation endproduct receptor signaling / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Amyloidogenic glycoprotein extracellular domain signature. / Pancreatic trypsin inhibitor (Kunitz) family signature. / Amyloid fiber formation / E2 domain of amyloid precursor protein / Amyloidogenic glycoprotein intracellular domain signature. / Copper-binding of amyloid precursor, CuBD / TRAF6 mediated NF-kB activation / Post-translational protein phosphorylation / beta-amyloid precursor protein C-terminus / Pancreatic trypsin inhibitor (Kunitz) family profile. / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Beta-amyloid peptide (beta-APP) / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Amyloid A4 N-terminal heparin-binding / Platelet degranulation / Kunitz/Bovine pancreatic trypsin inhibitor domain / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of cellular response to tunicamycin / positive regulation of cellular response to thapsigargin / positive regulation of protein import / positive regulation of G-protein coupled receptor internalization / regulation of acetylcholine-gated cation channel activity / amylin binding / heparan sulfate binding / positive regulation of response to endoplasmic reticulum stress / receptor activator activity / positive regulation of 1-phosphatidylinositol-3-kinase activity / regulation of response to calcium ion / endosome to plasma membrane transport vesicle / acetylcholine receptor activator activity / collateral sprouting in absence of injury / regulation of dendritic spine maintenance / cellular response to norepinephrine stimulus / lipoprotein particle / synaptic growth at neuromuscular junction / positive regulation of oxidative stress-induced neuron death / microglia development / growth cone lamellipodium / negative regulation of mitochondrion organization / mating behavior / regulation of synapse structure or activity / regulation of amyloid fibril formation / protein trimerization / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte projection / regulation of epidermal growth factor-activated receptor activity / cellular process / growth cone filopodium / regulation of spontaneous synaptic transmission / axo-dendritic transport / axon midline choice point recognition / tumor necrosis factor production / astrocyte activation involved in immune response / positive regulation of astrocyte activation / intermediate-density lipoprotein particle / positive regulation of amyloid fibril formation / PTB domain binding / suckling behavior / modulation of excitatory postsynaptic potential / positive regulation of microglial cell activation / go:0030816: / amyloid-beta complex / neuron remodeling / acetylcholine receptor binding / positive regulation of G-protein coupled receptor protein signaling pathway / activation of MAPKKK activity / main axon / positive regulation of amyloid-beta formation / ciliary rootlet / positive regulation of cell activation / high-density lipoprotein particle / lipoprotein metabolic process / peptidase activator activity
Function and homology information
SourceHomo sapiens (human)
Methodelectron crystallography / cryo EM
AuthorsKrotee P / Griner SL / Sawaya MR / Cascio D / Rodriguez JA / Shi D / Philipp S / Murray K / Saelices L / Lee J / Seidler P / Glabe CG / Jiang L / Gonen T / Eisenberg DS
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Common fibrillar spines of amyloid-β and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors.
Authors: Pascal Krotee / Sarah L Griner / Michael R Sawaya / Duilio Cascio / Jose A Rodriguez / Dan Shi / Stephan Philipp / Kevin Murray / Lorena Saelices / Ji Lee / Paul Seidler / Charles G Glabe / Lin Jiang / Tamir Gonen / David S Eisenberg
Abstract: Amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) aggregate to form amyloid fibrils that deposit in tissues and are associated with Alzheimer's disease (AD) and type II diabetes (T2D), ...Amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) aggregate to form amyloid fibrils that deposit in tissues and are associated with Alzheimer's disease (AD) and type II diabetes (T2D), respectively. Individuals with T2D have an increased risk of developing AD, and conversely, AD patients have an increased risk of developing T2D. Evidence suggests that this link between AD and T2D might originate from a structural similarity between aggregates of Aβ and hIAPP. Using the cryoEM method microelectron diffraction, we determined the atomic structures of 11-residue segments from both Aβ and hIAPP, termed Aβ(24-34) WT and hIAPP(19-29) S20G, with 64% sequence similarity. We observed a high degree of structural similarity between their backbone atoms (0.96-Å root mean square deviation). Moreover, fibrils of these segments induced amyloid formation through self- and cross-seeding. Furthermore, inhibitors designed for one segment showed cross-efficacy for full-length Aβ and hIAPP and reduced cytotoxicity of both proteins, although by apparently blocking different cytotoxic mechanisms. The similarity of the atomic structures of Aβ(24-34) WT and hIAPP(19-29) S20G offers a molecular model for cross-seeding between Aβ and hIAPP.
Validation ReportPDB-ID: 5vos

SummaryFull reportAbout validation report
DateDeposition: May 3, 2017 / Header (metadata) release: Jul 19, 2017 / Map release: Jan 3, 2018 / Last update: Jun 6, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5vos
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_8720.map.gz (map file in CCP4 format, 217 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
14 pix
0.39 Å/pix.
= 4.699 Å
53 pix
0.47 Å/pix.
= 18.7 Å
73 pix
0.46 Å/pix.
= 33.466 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.4675 Å / Y: 0.3916 Å / Z: 0.4648 Å
Density
Contour Level:0.3 (by emdb), 0.3 (movie #1):
Minimum - Maximum-0.61619514 - 1.0237845
Average (Standard dev.)0.0034368462 (0.20555635)
Details

EMDB XML:

Space Group Number4
Map Geometry
Axis orderZXY
Dimensions537314
Origin-1265-8
Limit401375
Spacing401272
CellA: 18.7 Å / B: 4.6992 Å / C: 33.4656 Å
α: 90.0 deg. / β: 100.017 deg. / γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.46750.391583333333330.46480555555556
M x/y/z401272
origin x/y/z0.0000.0000.000
length x/y/z18.7004.69933.466
α/β/γ90.000100.01790.000
start NX/NY/NZ-12-865
NX/NY/NZ531473
MAP C/R/S312
start NC/NR/NS65-12-8
NC/NR/NS735314
D min/max/mean-0.6161.0240.003

-
Supplemental data

-
Sample components

-
Entire Fibrils of Amyloid Beta segment 24-34

EntireName: Fibrils of Amyloid Beta segment 24-34 / Number of components: 3

-
Component #1: protein, Fibrils of Amyloid Beta segment 24-34

ProteinName: Fibrils of Amyloid Beta segment 24-34 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

-
Component #2: protein, Amyloid beta A4 protein

ProteinName: Amyloid beta A4 protein / Recombinant expression: No
MassTheoretical: 1.029213 kDa

-
Component #3: ligand, water

LigandName: water / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: 3D array / Method: cryo EM
Crystal parametersSpace group: P 21 / A: 18.78 Å / B: 4.73 Å / C: 33.47 Å / Alpha: 90 deg. / Beta: 100.017 deg. / Gamma: 90 deg.
Crystal grow detailsshaking
Sample solutionSpecimen conc.: 7.5 mg/ml / pH: 4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.03 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DIFFRACTION
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

-
Image processing

ProcessingMethod: electron crystallography
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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