+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15781 | |||||||||
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Title | 2C9, C5b9-CD59 cryoEM structure | |||||||||
Map data | Locally filtered 2C9-CD59 map | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of activation of membrane attack complex / cell killing / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / other organism cell membrane / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis ...negative regulation of activation of membrane attack complex / cell killing / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / other organism cell membrane / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / Cargo concentration in the ER / complement activation, alternative pathway / complement activation / chemokine activity / COPII-mediated vesicle transport / retinol binding / endopeptidase inhibitor activity / tertiary granule membrane / positive regulation of vascular endothelial growth factor production / specific granule membrane / COPI-mediated anterograde transport / positive regulation of chemokine production / transport vesicle / complement activation, classical pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / Peptide ligand-binding receptors / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / protein homooligomerization / chemotaxis / positive regulation of immune response / blood coagulation / extracellular vesicle / G alpha (i) signalling events / vesicle / in utero embryonic development / killing of cells of another organism / blood microparticle / cell surface receptor signaling pathway / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / Golgi membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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_15781.map.gz | 331.6 MB | EMDB map data format | |
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Header (meta data) | emd-15781-v30.xml emd-15781.xml | 31.5 KB 31.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15781_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_15781.png | 39.8 KB | ||
Masks | emd_15781_msk_1.map | 600.7 MB | Mask map | |
Others | emd_15781_additional_1.map.gz emd_15781_half_map_1.map.gz emd_15781_half_map_2.map.gz | 485.5 MB 483.6 MB 484.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15781 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15781 | HTTPS FTP |
-Validation report
Summary document | emd_15781_validation.pdf.gz | 781 KB | Display | EMDB validaton report |
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Full document | emd_15781_full_validation.pdf.gz | 780.5 KB | Display | |
Data in XML | emd_15781_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | emd_15781_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15781 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15781 | HTTPS FTP |
-Related structure data
Related structure data | 8b0hMC 8b0fC 8b0gC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15781.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Locally filtered 2C9-CD59 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
-Mask #1
File | emd_15781_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Relion refinement map of 2C9-CD59 (full structure)
File | emd_15781_additional_1.map | ||||||||||||
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Annotation | Relion refinement map of 2C9-CD59 (full structure) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion refinement map of 2C9-CD59 (full structure) unfiltered...
File | emd_15781_half_map_1.map | ||||||||||||
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Annotation | Relion refinement map of 2C9-CD59 (full structure) unfiltered half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Relion refinement map of 2C9-CD59 (full structure) unfiltered...
File | emd_15781_half_map_2.map | ||||||||||||
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Annotation | Relion refinement map of 2C9-CD59 (full structure) unfiltered half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 2C9, CD59 inhibited MAC Complex
+Supramolecule #1: 2C9, CD59 inhibited MAC Complex
+Supramolecule #2: CD59 glycoprotein
+Supramolecule #3: Complement components C5, C6, C7, C8 and C9
+Macromolecule #1: CD59 glycoprotein
+Macromolecule #2: Complement component C8 beta chain
+Macromolecule #3: Complement component C8 gamma chain
+Macromolecule #4: Complement component C8 alpha chain
+Macromolecule #5: Complement C5
+Macromolecule #6: Complement component C7
+Macromolecule #7: Complement component C6
+Macromolecule #8: Complement component C9
-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 / Material: COPPER / Mesh: 300 / 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 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |