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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1991 | |||||||||
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Title | Structure of complement component complex, sC5b9. | |||||||||
![]() | This is an image of a surface rendered view of the sC5b9 complex | |||||||||
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![]() | complement terminal pathway / humoral immune pore / MACPF domain | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 24.0 Å | |||||||||
![]() | Bubeck D / Roversi P / Hakabyan S / Morgan BP / Lea SM / Llorca O | |||||||||
![]() | ![]() Title: Assembly and regulation of the membrane attack complex based on structures of C5b6 and sC5b9. Authors: Michael A Hadders / Doryen Bubeck / Pietro Roversi / Svetlana Hakobyan / Federico Forneris / B Paul Morgan / Michael K Pangburn / Oscar Llorca / Susan M Lea / Piet Gros / ![]() Abstract: Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal ...Activation of the complement system results in formation of membrane attack complexes (MACs), pores that disrupt lipid bilayers and lyse bacteria and other pathogens. Here, we present the crystal structure of the first assembly intermediate, C5b6, together with a cryo-electron microscopy reconstruction of a soluble, regulated form of the pore, sC5b9. Cleavage of C5 to C5b results in marked conformational changes, distinct from those observed in the homologous C3-to-C3b transition. C6 captures this conformation, which is preserved in the larger sC5b9 assembly. Together with antibody labeling, these structures reveal that complement components associate through sideways alignment of the central MAC-perforin (MACPF) domains, resulting in a C5b6-C7-C8β-C8α-C9 arc. Soluble regulatory proteins below the arc indicate a potential dual mechanism in protection from pore formation. These results provide a structural framework for understanding MAC pore formation and regulation, processes important for fighting infections and preventing complement-mediated tissue damage. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 11.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.9 KB 12.9 KB | Display Display | ![]() |
Images | ![]() | 123.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an image of a surface rendered view of the sC5b9 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : sC5b9
Entire | Name: sC5b9 |
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Components |
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-Supramolecule #1000: sC5b9
Supramolecule | Name: sC5b9 / type: sample / ID: 1000 / Details: The sample was monodisperse Oligomeric state: 7, C8, and C9. In addition it contains clusterin and vitronectin with an unknown stoichiometry. Number unique components: 7 |
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-Macromolecule #1: C5b
Macromolecule | Name: C5b / type: protein_or_peptide / ID: 1 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Macromolecule #2: C6
Macromolecule | Name: C6 / type: protein_or_peptide / ID: 2 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Macromolecule #3: C7
Macromolecule | Name: C7 / type: protein_or_peptide / ID: 3 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Macromolecule #4: C8
Macromolecule | Name: C8 / type: protein_or_peptide / ID: 4 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Macromolecule #5: C9
Macromolecule | Name: C9 / type: protein_or_peptide / ID: 5 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Macromolecule #6: Clusterin
Macromolecule | Name: Clusterin / type: protein_or_peptide / ID: 6 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Macromolecule #7: vibronectin
Macromolecule | Name: vibronectin / type: protein_or_peptide / ID: 7 / Name.synonym: sC5b9, or sMAC / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 / Details: 150mM NaCl, 50mM Tris, 1mM CaCl2, and 1mM MgCl2 |
Grid | Details: quantifoil holey carbon grids |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot |
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Electron microscopy
Microscope | JEOL 2200FS |
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Specialist optics | Energy filter - Name: OMEGA |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 405 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 54400 |
Sample stage | Specimen holder: single-tilt cryo holder / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: Bsoft, phase flip on each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, XMIPP / Number images used: 18983 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
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Software | Name: ![]() |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient |