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- EMDB-24144: ApoL3, A human apolipoprotein L -

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Basic information

Entry
Database: EMDB / ID: EMD-24144
TitleApoL3, A human apolipoprotein L
Map dataApoL3 nanodisc in low resolution because of non-sufficient order.
Sample
  • Organelle or cellular component: APOL3 lipoprotein in complex with DMPC/DMPG (75:25) lipid
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsZhu S / MacMicking J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI068041-14 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI108834-07 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2021
Title: A human apolipoprotein L with detergent-like activity kills intracellular pathogens.
Authors: Ryan G Gaudet / Shiwei Zhu / Anushka Halder / Bae-Hoon Kim / Clinton J Bradfield / Shuai Huang / Dijin Xu / Agnieszka Mamiñska / Thanh Ngoc Nguyen / Michael Lazarou / Erdem Karatekin / ...Authors: Ryan G Gaudet / Shiwei Zhu / Anushka Halder / Bae-Hoon Kim / Clinton J Bradfield / Shuai Huang / Dijin Xu / Agnieszka Mamiñska / Thanh Ngoc Nguyen / Michael Lazarou / Erdem Karatekin / Kallol Gupta / John D MacMicking /
Abstract: Activation of cell-autonomous defense by the immune cytokine interferon-γ (IFN-γ) is critical to the control of life-threatening infections in humans. IFN-γ induces the expression of hundreds of ...Activation of cell-autonomous defense by the immune cytokine interferon-γ (IFN-γ) is critical to the control of life-threatening infections in humans. IFN-γ induces the expression of hundreds of host proteins in all nucleated cells and tissues, yet many of these proteins remain uncharacterized. We screened 19,050 human genes by CRISPR-Cas9 mutagenesis and identified IFN-γ-induced apolipoprotein L3 (APOL3) as a potent bactericidal agent protecting multiple non-immune barrier cell types against infection. Canonical apolipoproteins typically solubilize mammalian lipids for extracellular transport; APOL3 instead targeted cytosol-invasive bacteria to dissolve their anionic membranes into human-bacterial lipoprotein nanodiscs detected by native mass spectrometry and visualized by single-particle cryo-electron microscopy. Thus, humans have harnessed the detergent-like properties of extracellular apolipoproteins to fashion an intracellular lysin, thereby endowing resident nonimmune cells with a mechanism to achieve sterilizing immunity.
History
DepositionJun 1, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00363
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00363
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24144.png

Downloads & links

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Map

FileDownload / File: emd_24144.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoL3 nanodisc in low resolution because of non-sufficient order.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 256 pix.
= 229.376 Å		0.9 Å/pix.
x 256 pix.
= 229.376 Å		0.9 Å/pix.
x 256 pix.
= 229.376 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.896 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00363 / Movie #1: 0.00363
Minimum - Maximum-0.002197717 - 0.0072414377
Average (Standard dev.)0.00022444186 (±0.00094840815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 229.376 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8960.8960.896
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z229.376229.376229.376
α/β/γ90.00090.00090.000
start NX/NY/NZ7371100
NX/NY/NZ11585169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0020.0070.000

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Supplemental data

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Sample components

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Entire : APOL3 lipoprotein in complex with DMPC/DMPG (75:25) lipid

EntireName: APOL3 lipoprotein in complex with DMPC/DMPG (75:25) lipid
Components
  • Organelle or cellular component: APOL3 lipoprotein in complex with DMPC/DMPG (75:25) lipid

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Supramolecule #1: APOL3 lipoprotein in complex with DMPC/DMPG (75:25) lipid

SupramoleculeName: APOL3 lipoprotein in complex with DMPC/DMPG (75:25) lipid
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 236364
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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