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- EMDB-8720: VGSNKGAIIGL from Amyloid Beta determined by MicroED -

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Basic information

Entry
Database: EMDB / ID: 8720
TitleVGSNKGAIIGL from Amyloid Beta determined by MicroED
SampleFibrils of Amyloid Beta segment 24-34
SourceHomo sapiens / human
Map dataVGSNKGAIIGL from Amyloid Beta
Methodelectron crystallography
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
CitationJ. Biol. Chem., 2017

J. Biol. Chem., 2017 Yorodumi Papers
Common fibrillar spines of amyloid-β and human Islet Amyloid Polypeptide revealed by Micro Electron Diffraction and inhibitors developed using structure-based design.
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

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: Jan 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5vos
  • Surface level: 0.3
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

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

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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 package.

(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 deg. / β: 100.017 deg. / γ: 90 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

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Supplemental data

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Sample components

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Entire Fibrils of Amyloid Beta segment 24-34

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

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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

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Component #2: protein, Amyloid beta A4 protein

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

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Component #3: ligand, water

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

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Experimental details

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Sample preparation

Specimen state3D array
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

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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)

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Image processing

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

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Atomic model buiding

Output model

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