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- EMDB-6186: Electron cryo-microscopy of Terebralia palustris mega-hemocyanin -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6186 | |||||||||
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Title | Electron cryo-microscopy of Terebralia palustris mega-hemocyanin | |||||||||
![]() | Reconstruction of Terebralia palustris mega-hemocyanin | |||||||||
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![]() | oxygen transport / origami | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.4 Å | |||||||||
![]() | Gatsogiannis C / Hofnagel O / Markl J / Raunser S | |||||||||
![]() | ![]() Title: Structure of mega-hemocyanin reveals protein origami in snails. Authors: Christos Gatsogiannis / Oliver Hofnagel / Jürgen Markl / Stefan Raunser / ![]() Abstract: Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional ...Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional 550 kDa subunits. Together, they form a large, completely filled cylinder. The structural basis for this highly complex protein packing is not known so far. Here, we report the electron cryomicroscopy (cryo-EM) structure of mega-hemocyanin complexes from two different snail species. The structures reveal that mega-hemocyanin is composed of flexible building blocks that differ in their conformation, but not in their primary structure. Like a protein origami, these flexible blocks are optimally packed, implementing different local symmetries and pseudosymmetries. A comparison between the two structures suggests a surprisingly simple evolutionary mechanism leading to these large oxygen transporters. | |||||||||
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 | ![]() | 95 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.4 KB 10.4 KB | Display Display | ![]() |
Images | ![]() | 725.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78 KB | Display | ![]() |
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Full document | ![]() | 77 KB | Display | |
Data in XML | ![]() | 495 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Terebralia palustris mega-hemocyanin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.51 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 : Terebralia palustris Mega-Hemocyanin (TpH)
Entire | Name: Terebralia palustris Mega-Hemocyanin (TpH) |
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Components |
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-Supramolecule #1000: Terebralia palustris Mega-Hemocyanin (TpH)
Supramolecule | Name: Terebralia palustris Mega-Hemocyanin (TpH) / type: sample / ID: 1000 Oligomeric state: Two peripheral decamers of the short TpH subunit with 8FUs bind to a central decamer of the long TpH subunit with 11 FUs. Number unique components: 2 |
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Molecular weight | Experimental: 13 MDa / Theoretical: 13 MDa |
-Macromolecule #1: Mega-hemocyanin long-chain
Macromolecule | Name: Mega-hemocyanin long-chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Decamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 5 MDa / Theoretical: 5 MDa |
-Macromolecule #2: Mega-hemocyanin short-chain
Macromolecule | Name: Mega-hemocyanin short-chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Oligomeric state: Decamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 4 MDa / Theoretical: 4 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 Details: 50 mM Tris-HCl, 150 mM NaCl, 5 mM CaCl2, 5 mM MgCl2 |
Grid | Details: C-Flat 2/1-4C copper 400 mesh, with additional thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 3 seconds before plunging. |
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Electron microscopy
Microscope | JEOL 3200FSC |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification. |
Specialist optics | Energy filter - Name: in-column Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV |
Date | Mar 10, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 1636 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 124472 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
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Image processing
Details | C5 symmetry was imposed locally after each iteration during the refinement. |
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CTF correction | Details: each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: OTHER / Software - Name: SPARX / Number images used: 30527 |