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- EMDB-2503: Cryo-EM Structure of Isomeric Molluscan Hemocyanin Type 1 trigger... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2503 | |||||||||
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Title | Cryo-EM Structure of Isomeric Molluscan Hemocyanin Type 1 triggered by viral infection | |||||||||
![]() | Reconstruction of isomeric Halitotis diversicolor hemocyanin type 1 triggered by AbSV | |||||||||
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![]() | isomeric molluscan hemocyanin / viral infection / AbSV / phenoloxidase | |||||||||
Function / homology | ![]() : / oxygen carrier activity / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
![]() | Zhu HT / Zhuang J / Feng HL / Liang RF / Wang JY / Xie LH / Zhu P | |||||||||
![]() | ![]() Title: Cryo-EM structure of isomeric molluscan hemocyanin triggered by viral infection. Authors: Hongtao Zhu / Jun Zhuang / Hongli Feng / Rongfeng Liang / Jiangyong Wang / Lianhui Xie / Ping Zhu / ![]() Abstract: Hemocyanins (Hcs) of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs). In invertebrates, PO is an important component in the innate immune cascade, ...Hemocyanins (Hcs) of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs). In invertebrates, PO is an important component in the innate immune cascade, where it functions as the initiator of melanin synthesis, a pigment involved in encapsulating and killing of pathogenic microbes. Although structures of Hc from several species of invertebrates have been reported, the structural basis for how PO activity is triggered by structural changes of Hc in vivo remains poorly understood. Here, we report a 6.8 Å cryo-electron microscopy (cryo-EM) structure of the isomeric form of hemocyanin, which was isolated from Abalone Shriveling syndrome-associated Virus (AbSV) infected abalone (Halitotis diversicolor), and build a pseudoatomic model of isomeric H. diversicolor hemocyanin 1 (HdH1). Our results show that, compared with native form of HdH1, the architecture of isomeric HdH1 turns into a more relaxed form. The interactions between certain functional units (FUs) present in the native form of Hc either decreased or were totally abolished in the isomeric form of Hc. As a result of that, native state Hc switches to its isomeric form, enabling it to play its role in innate immune responses against invading pathogens. | |||||||||
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 | ![]() | 226.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.3 KB 9.3 KB | Display Display | ![]() |
Images | ![]() | 311.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of isomeric Halitotis diversicolor hemocyanin type 1 triggered by AbSV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.196 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 : Isomeric Molluscan Hemocyanin triggered by AbSV infection
Entire | Name: Isomeric Molluscan Hemocyanin triggered by AbSV infection |
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Components |
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-Supramolecule #1000: Isomeric Molluscan Hemocyanin triggered by AbSV infection
Supramolecule | Name: Isomeric Molluscan Hemocyanin triggered by AbSV infection type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 8 MDa |
-Macromolecule #1: isomeric hemocyanin type 1
Macromolecule | Name: isomeric hemocyanin type 1 / type: protein_or_peptide / ID: 1 / Name.synonym: HdH1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8 MDa |
Sequence | UniProtKB: Hemocyanin isoform 1 / GO: GO: 0055114 / InterPro: Di-copper centre-containing domain superfamily |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.8 / Details: 20mM phosphate buffer, containing 2.5mM MgCl2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 125418 times magnification |
Specialist optics | Energy filter - Name: FEI |
Date | Dec 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 2379 / Average electron dose: 18 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 125418 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | EMAN2 was initially used for particle picking, 2D classification, projection refinement and 3D reconstruction for both normal and isomeric hemocyanins with C5 symmetry imposed. Subsequently, 57,043 isomeric hemocyanin particles were imported to Relion-1.1 for further refinement and reconstruction by applying D5 symmetry, using the reconstructed map from EMAN2 as the initial model. Xmipp-2.4 was used for the? bfactor correction to generate the final 3D reconstruction map of isomeric hemocyanin. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: OTHER / Software - Name: EMAN2, Relion-1.1, Xmipp-2.4 / Number images used: 57043 |