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Yorodumi- EMDB-5585: Electron cryo-microscopy of Haliotis diversicolor molluscan hemoc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5585 | |||||||||
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Title | Electron cryo-microscopy of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) | |||||||||
Map data | Reconstruction of isolated Haliotis diversicolor molluscan hemocyanin isoform 1 | |||||||||
Sample |
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Keywords | Cryo-EM / molluscan hemocyanin / Allosteric | |||||||||
Biological species | Haliotis diversicolor (invertebrata) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Zhang Q / Dai X / Cong Y / Zhang J / Chen DH / Dougherty M / Wang J / Ludtke S / Schmid MF / Chiu W | |||||||||
Citation | Journal: Structure / Year: 2013 Title: Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism. Authors: Qinfen Zhang / Xinghong Dai / Yao Cong / Junjie Zhang / Dong-Hua Chen / Matthew T Dougherty / Jiangyong Wang / Steven J Ludtke / Michael F Schmid / Wah Chiu / Abstract: Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of ...Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of eight functional units (FUs). Each FU contains two Cu ions, which can reversibly bind an oxygen molecule. Here, we report a 4.5 A° cryo-EM structure of HdH1. The structure clearly shows ten asymmetric units arranged with D5 symmetry. Each asymmetric unit contains two structurally distinct but chemically identical subunits. The map is sufficiently resolved to trace the entire subunit Ca backbone and to visualize densities corresponding to some large side chains, Cu ion pairs, and interaction networks of adjacent subunits. A FU topology path intertwining between the two subunits of the asymmetric unit is unambiguously determined. Our observations suggest a structural mechanism for the stability of the entire hemocyanin didecamer and 20 ‘‘communication clusters’’ across asymmetric units responsible for its allosteric property upon oxygen binding. | |||||||||
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_5585.map.gz | 50.5 MB | EMDB map data format | |
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Header (meta data) | emd-5585-v30.xml emd-5585.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_5585_1.png | 355.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5585 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5585 | HTTPS FTP |
-Validation report
Summary document | emd_5585_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_5585_full_validation.pdf.gz | 78.3 KB | Display | |
Data in XML | emd_5585_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5585 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5585 | HTTPS FTP |
-Related structure data
Related structure data | 1648C 5586C 3j32FC F: fitted*YM 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_5585.map.gz / Format: CCP4 / Size: 804.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of isolated Haliotis diversicolor molluscan hemocyanin isoform 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 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 : Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Entire | Name: Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) |
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Components |
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-Supramolecule #1000: Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Supramolecule | Name: Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: one didecamer of HdH1 / Number unique components: 1 |
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Molecular weight | Experimental: 8 MDa / Theoretical: 8 MDa |
-Macromolecule #1: hemocyanin isoform 1
Macromolecule | Name: hemocyanin isoform 1 / type: protein_or_peptide / ID: 1 / Name.synonym: HdH1 / Number of copies: 10 / Oligomeric state: didecamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Haliotis diversicolor (invertebrata) / synonym: mollusca / Tissue: lymph |
Molecular weight | Experimental: 8 MDa / Theoretical: 8 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2 |
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Grid | Details: 400 mesh copper 1.2/1.3 quantifoil grid with continuous carbon support, glow discharged. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 2 seconds before plunging. |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 80 K / Max: 100 K / Average: 88 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 nominal magnification |
Specialist optics | Energy filter - Name: in column omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | MDS |
Date | Jul 7, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 784 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: liquid N2 cooled / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
Details | EMAN1 |
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CTF correction | Details: each micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 28641 |