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Yorodumi- EMDB-0111: Asymmetric region of the Membrane Attack Complex in the open conf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0111 | |||||||||
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Title | Asymmetric region of the Membrane Attack Complex in the open conformation | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Menny A / Serna M / Boyd CB / Gardener S / Joseph AP / Topf M / Bubeck D | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers. Authors: Anaïs Menny / Marina Serna / Courtney M Boyd / Scott Gardner / Agnel Praveen Joseph / B Paul Morgan / Maya Topf / Nicholas J Brooks / Doryen Bubeck / Abstract: The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of ...The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of self-cells. How MAC disrupts the membrane barrier remains unclear. Here we use electron cryo-microscopy and flicker spectroscopy to show that MAC interacts with lipid bilayers in two distinct ways. Whereas C6 and C7 associate with the outer leaflet and reduce the energy for membrane bending, C8 and C9 traverse the bilayer increasing membrane rigidity. CryoEM reconstructions reveal plasticity of the MAC pore and demonstrate how C5b6 acts as a platform, directing assembly of a giant β-barrel whose structure is supported by a glycan scaffold. Our work provides a structural basis for understanding how β-pore forming proteins breach the membrane and reveals a mechanism for how MAC kills pathogens and regulates cell functions. | |||||||||
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_0111.map.gz | 102.2 MB | EMDB map data format | |
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Header (meta data) | emd-0111-v30.xml emd-0111.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_0111.png | 51.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0111 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0111 | HTTPS FTP |
-Validation report
Summary document | emd_0111_validation.pdf.gz | 209.6 KB | Display | EMDB validaton report |
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Full document | emd_0111_full_validation.pdf.gz | 208.7 KB | Display | |
Data in XML | emd_0111_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0111 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0111 | HTTPS FTP |
-Related structure data
Related structure data | 0106C 0107C 0109C 0110C 0112C 0113C 6h03C 6h04C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0111.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.384 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Membrane Attack Complex
Entire | Name: Membrane Attack Complex |
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Components |
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-Supramolecule #1: Membrane Attack Complex
Supramolecule | Name: Membrane Attack Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 Details: Protein complex was assembled on liposomes and detergent solubilized |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 69 KDa |
-Supramolecule #2: C5b
Supramolecule | Name: C5b / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Component of the Membrane Attack Complex |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: C6
Supramolecule | Name: C6 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Component of the Membrane Attack Complex |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #4: C7
Supramolecule | Name: C7 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4 / Details: Component of the Membrane Attack Complex |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #5: C8 alpha
Supramolecule | Name: C8 alpha / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6 / Details: Component of the Membrane Attack Complex |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #6: C8 beta
Supramolecule | Name: C8 beta / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3 / Details: Component of the Membrane Attack Complex |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #7: C8 gamma
Supramolecule | Name: C8 gamma / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #5 / Details: Component of the Membrane Attack Complex |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #8: C9
Supramolecule | Name: C9 / type: complex / ID: 8 / Parent: 1 / Macromolecule list: #7 / Details: Component of the Membrane Attack Complex |
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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
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 8 / Number real images: 13009 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |