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Open data
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Basic information
Entry | Database: PDB / ID: 7nyd | ||||||||||||
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Title | cryoEM structure of 2C9-sMAC | ||||||||||||
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![]() | IMMUNE SYSTEM / Complement / MACPF / Membrane Attack Complex / CDC / pore forming | ||||||||||||
Function / homology | ![]() 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 / Peptide ligand-binding receptors / complement activation, classical pathway / 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 | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å | ||||||||||||
![]() | Menny, A. / Couves, E.C. / Bubeck, D. | ||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 985.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12651MC ![]() 7nycC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Complement component ... , 6 types, 7 molecules DEGHCBF
#1: Protein | Mass: 61122.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#2: Protein | Mass: 61782.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#3: Protein | Mass: 61056.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 91221.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 102541.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | | Mass: 20410.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein / Non-polymers , 2 types, 5 molecules A![](data/chem/img/CA.gif)
![](data/chem/img/CA.gif)
#12: Chemical | ChemComp-CA / #7: Protein | | Mass: 186546.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 6 types, 13 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/FUC.gif)
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![](data/chem/img/FUC.gif)
#8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#9: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#11: Sugar | ChemComp-MAN / #13: Sugar | #14: Sugar | ChemComp-FUC / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 2C9-sMAC / Type: COMPLEX 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 Entity ID: #1-#7 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.065 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: REFMAC / Version: 5.8.0253 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142499 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 3.27→3.27 Å / Cor.coef. Fo:Fc: 0.881 / SU B: 11.519 / SU ML: 0.167 / ESU R: 0.117 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 202.736 Å2
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Refinement step | Cycle: 1 / Total: 38488 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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