+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15782 | |||||||||
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Title | 2C9, C5b9-CD59 cryoEM structure; focus refinement map | |||||||||
Map data | 2C9, C5b9-CD59 density subtracted map. RELION local resolution filtered map. | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Couves EC / Gardner S / Bubeck D | |||||||||
Funding support | European Union, United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for membrane attack complex inhibition by CD59. Authors: Emma C Couves / Scott Gardner / Tomas B Voisin / Jasmine K Bickel / Phillip J Stansfeld / Edward W Tate / Doryen Bubeck / Abstract: CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to ...CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to prevent insertion and polymerization of membrane attack complex (MAC) pores. We present cryo-electron microscopy structures of two inhibited MAC precursors known as C5b8 and C5b9. We discover that in both complexes, CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane. Preventing insertion of C9 restricts structural transitions of subsequent monomers and indirectly halts MAC polymerization. We combine our structural data with cellular assays and molecular dynamics simulations to explain how the membrane environment impacts the dual roles of CD59 in controlling pore formation of MAC, and as a target of bacterial virulence factors which hijack CD59 to lyse human cells. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15782.map.gz | 328.6 MB | EMDB map data format | |
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Header (meta data) | emd-15782-v30.xml emd-15782.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15782_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_15782.png | 46.2 KB | ||
Others | emd_15782_half_map_1.map.gz emd_15782_half_map_2.map.gz | 484 MB 483.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15782 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15782 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15782.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 2C9, C5b9-CD59 density subtracted map. RELION local resolution filtered map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.831 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: 2C9, C5b9-CD59 density subtracted map. RELION unfiltered half map.
File | emd_15782_half_map_1.map | ||||||||||||
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Annotation | 2C9, C5b9-CD59 density subtracted map. RELION unfiltered half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 2C9, C5b9-CD59 density subtracted map. RELION unfiltered half map.
File | emd_15782_half_map_2.map | ||||||||||||
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Annotation | 2C9, C5b9-CD59 density subtracted map. RELION unfiltered half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 2C9, CD59 inhibited MAC Complex
Entire | Name: 2C9, CD59 inhibited MAC Complex |
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Components |
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-Supramolecule #1: 2C9, CD59 inhibited MAC Complex
Supramolecule | Name: 2C9, CD59 inhibited MAC Complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#9 Details: Solved in a DOPC, MSP2N2 nanodisc with a myristolated cytotopic CD59. |
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Source (natural) | Organism: Homo sapiens (human) / Location in cell: Serum |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: 20 mM HEPES pH 7.4, 120 mM NaCl | |||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK II | |||||||||
Details | C5b, C6, C7, C8 and C9 purified components were sources from CompTech. Myrisolated CD59 was a gift from R. Smith. Individual components were reacted together empty DOPC nanodiscs then purified by sucrose gradient centrifugation. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 52838 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Collected over 4 separate data collections |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |