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Open data
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Basic information
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Title | CryoEM structure of C5b8-CD59 | |||||||||
![]() | CryoEM reconstruction of C5b8-CD59. | |||||||||
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Function / homology | ![]() negative regulation of activation of membrane attack complex / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / Cargo concentration in the ER / complement activation, alternative pathway ...negative regulation of activation of membrane attack complex / Terminal pathway of complement / membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / 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 / COPI-mediated anterograde transport / specific granule membrane / positive regulation of chemokine production / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / Peptide ligand-binding receptors / complement activation, classical pathway / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / chemotaxis / positive regulation of immune response / extracellular vesicle / blood coagulation / G alpha (i) signalling events / in utero embryonic development / vesicle / killing of cells of another organism / cell surface receptor signaling pathway / blood microparticle / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Bubeck D / Couves EC / Gardner S | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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. #1: ![]() Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 281.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.5 KB 30.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.7 KB | Display | ![]() |
Images | ![]() | 100.9 KB | ||
Masks | ![]() | 343 MB | ![]() | |
Others | ![]() ![]() | 318.7 MB 318.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 649.3 KB | Display | ![]() |
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Full document | ![]() | 648.9 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b0fMC ![]() 8b0gC ![]() 8b0hC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoEM reconstruction of C5b8-CD59. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.171 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: CryoEM reconstruction of C5b8-CD59.
File | emd_15779_half_map_1.map | ||||||||||||
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Annotation | CryoEM reconstruction of C5b8-CD59. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM reconstruction of C5b8-CD59.
File | emd_15779_half_map_2.map | ||||||||||||
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Annotation | CryoEM reconstruction of C5b8-CD59. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : C5b8-CD59
+Supramolecule #1: C5b8-CD59
+Supramolecule #2: Complement components C5, C6, C7 and C8
+Supramolecule #3: CD59 glycoprotein
+Macromolecule #1: Complement C5
+Macromolecule #2: Complement component C6
+Macromolecule #3: Complement component C7
+Macromolecule #4: Complement component C8 beta chain
+Macromolecule #5: Complement component C8 alpha chain
+Macromolecule #6: Complement component C8 gamma chain
+Macromolecule #7: CD59 glycoprotein
+Macromolecule #10: CALCIUM ION
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: NITROGEN |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 12805 / Average exposure time: 9.8 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Initial rigid body fits were performed using UCSF Chimera and UCSF ChimeraX. Carbohydrates were added using Coot. Models were refined iteratively using Isolde and Phenix Real Space Refine. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87 |
Output model | ![]() PDB-8b0f: |