+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12647 | ||||||||||||
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Title | cryoEM reconstruction of the terminal C9s in 2C9-sMAC | ||||||||||||
Map data | Locally sharpened reconstruction of 2C9-sMAC density subtracted and focused on C9 | ||||||||||||
Sample |
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Function / homology | Function and homology information cell killing / Terminal pathway of complement / membrane attack complex / complement binding / other organism cell membrane / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / complement activation / chemokine activity ...cell killing / Terminal pathway of complement / membrane attack complex / complement binding / other organism cell membrane / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / complement activation / chemokine activity / retinol binding / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / complement activation, classical pathway / Peptide ligand-binding receptors / Regulation of Complement cascade / protein homooligomerization / chemotaxis / positive regulation of immune response / extracellular vesicle / G alpha (i) signalling events / 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 / innate immune response / signaling receptor binding / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||||||||
Authors | Menny A / Couves EC / Bubeck D | ||||||||||||
Funding support | European Union, United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of soluble membrane attack complex packaging for clearance. Authors: Anaïs Menny / Marie V Lukassen / Emma C Couves / Vojtech Franc / Albert J R Heck / Doryen Bubeck / Abstract: Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular ...Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular chaperones (clusterin and vitronectin) capture and clear soluble precursors to the membrane attack complex (sMAC). However, how these chaperones block further polymerization of MAC and prevent the complex from binding target membranes remains unclear. Here, we address that question by combining cryo electron microscopy (cryoEM) and cross-linking mass spectrometry (XL-MS) to solve the structure of sMAC. Together our data reveal how clusterin recognizes and inhibits polymerizing complement proteins by binding a negatively charged surface of sMAC. Furthermore, we show that the pore-forming C9 protein is trapped in an intermediate conformation whereby only one of its two transmembrane β-hairpins has unfurled. This structure provides molecular details for immune pore formation and helps explain a complement control mechanism that has potential implications for how cell clearance pathways mediate immune homeostasis. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12647.map.gz | 90.7 MB | EMDB map data format | |
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Header (meta data) | emd-12647-v30.xml emd-12647.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_12647.png | 68.8 KB | ||
Others | emd_12647_half_map_1.map.gz emd_12647_half_map_2.map.gz | 80.7 MB 80.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12647 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12647 | HTTPS FTP |
-Validation report
Summary document | emd_12647_validation.pdf.gz | 402.4 KB | Display | EMDB validaton report |
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Full document | emd_12647_full_validation.pdf.gz | 402 KB | Display | |
Data in XML | emd_12647_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_12647_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12647 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12647 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12647.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally sharpened reconstruction of 2C9-sMAC density subtracted and focused on C9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 1 of 2C9-sMAC density subtracted and focused on C9
File | emd_12647_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of 2C9-sMAC density subtracted and focused on C9 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of 2C9-sMAC density subtracted and focused on C9
File | emd_12647_half_map_2.map | ||||||||||||
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Annotation | Half map 2 of 2C9-sMAC density subtracted and focused on C9 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 2C9-sMAC
Entire | Name: 2C9-sMAC |
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Components |
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-Supramolecule #1: 2C9-sMAC
Supramolecule | Name: 2C9-sMAC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 Details: This sMAC oligomer contains one copy of C5b8 and 2 copies of C9, as well as multiple copies of the chaperones vitronectin and clusterin |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.065 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |