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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2506 | |||||||||
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Title | Cryo-electron tomography average of an C1-IgG complex | |||||||||
![]() | C1-IgG | |||||||||
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![]() | C1-IgG complex / C1-immune complex / C1 / C1qr2S2 / IgG / classical complement activation | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 66.0 Å | |||||||||
![]() | Diebolder CA / Beurskens FJ / de Jong RN / Koning RI / Strumane K / Lindorfer MA / Voorhorst M / Ugurlar D / Rosati S / Heck AJR ...Diebolder CA / Beurskens FJ / de Jong RN / Koning RI / Strumane K / Lindorfer MA / Voorhorst M / Ugurlar D / Rosati S / Heck AJR / van de Winkel JGJ / Wilson IA / Koster AJ / Taylor RP / Ollmann-Saphire E / Burton DR / Schuurman J / Gros P / Parren PWHI | |||||||||
![]() | ![]() Title: Complement is activated by IgG hexamers assembled at the cell surface. Authors: Christoph A Diebolder / Frank J Beurskens / Rob N de Jong / Roman I Koning / Kristin Strumane / Margaret A Lindorfer / Marleen Voorhorst / Deniz Ugurlar / Sara Rosati / Albert J R Heck / Jan ...Authors: Christoph A Diebolder / Frank J Beurskens / Rob N de Jong / Roman I Koning / Kristin Strumane / Margaret A Lindorfer / Marleen Voorhorst / Deniz Ugurlar / Sara Rosati / Albert J R Heck / Jan G J van de Winkel / Ian A Wilson / Abraham J Koster / Ronald P Taylor / Erica Ollmann Saphire / Dennis R Burton / Janine Schuurman / Piet Gros / Paul W H I Parren / ![]() Abstract: Complement activation by antibodies bound to pathogens, tumors, and self antigens is a critical feature of natural immune defense, a number of disease processes, and immunotherapies. How antibodies ...Complement activation by antibodies bound to pathogens, tumors, and self antigens is a critical feature of natural immune defense, a number of disease processes, and immunotherapies. How antibodies activate the complement cascade, however, is poorly understood. We found that specific noncovalent interactions between Fc segments of immunoglobulin G (IgG) antibodies resulted in the formation of ordered antibody hexamers after antigen binding on cells. These hexamers recruited and activated C1, the first component of complement, thereby triggering the complement cascade. The interactions between neighboring Fc segments could be manipulated to block, reconstitute, and enhance complement activation and killing of target cells, using all four human IgG subclasses. We offer a general model for understanding antibody-mediated complement activation and the design of antibody therapeutics with enhanced efficacy. | |||||||||
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 | ![]() | 3.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.1 KB 11.1 KB | Display Display | ![]() |
Images | ![]() | 223.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2507C ![]() 2554C C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 10.8 / Data #1: C1-IgG complex tilt series [class averages]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C1-IgG | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.3 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 : DNP-haptenated liposomes, polyclonal goat anti-DNP Antibody, huma...
Entire | Name: DNP-haptenated liposomes, polyclonal goat anti-DNP Antibody, human C1 (originating from C4 depleted serum) |
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Components |
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-Supramolecule #1000: DNP-haptenated liposomes, polyclonal goat anti-DNP Antibody, huma...
Supramolecule | Name: DNP-haptenated liposomes, polyclonal goat anti-DNP Antibody, human C1 (originating from C4 depleted serum) type: sample / ID: 1000 Oligomeric state: one C1 complex binds to one hexamer of membrane bound IgG Number unique components: 2 |
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Molecular weight | Theoretical: 1.65 MDa |
-Macromolecule #1: polyclonal IgG
Macromolecule | Name: polyclonal IgG / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #2: C1
Macromolecule | Name: C1 / type: protein_or_peptide / ID: 2 / Name.synonym: C1r2s2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 766 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Instrument: LEICA EM GP / Method: Blot 3 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan Quantum SE/963 |
Date | Jun 6, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 51 / Average electron dose: 100 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.5 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | particle selected using IMOD stalkInit. C6 for IgG hexamer (lower platform) C2 for C1r2s2 hetero tetramer (upper platform) |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 66.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET, Spider Details: Final map is an average of 107 particles, representing the first class after pca classification and k-means clustering of 200 particles. The 200 particles originate from ~50 single and dual axis tomograms Number subtomograms used: 107 |
CTF correction | Details: Phase flipping in IMOD after defocus esimation in TOMOCTF |