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Yorodumi- PDB-6r83: CryoEM structure and molecular model of squid hemocyanin (Todarod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r83 | ||||||||||||
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Title | CryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH) | ||||||||||||
Components | Hemocyanin subunit 1 | ||||||||||||
Keywords | OXYGEN TRANSPORT / oxygen transporter / mollusc / hemocyanin / copper / symmetry mismatch | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Todarodes pacificus (Japanese flying squid) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||
Authors | Tanaka, Y. / Kato, S. / Stabrin, M. / Raunser, S. / Matsui, T. / Gatsogiannis, C. | ||||||||||||
Funding support | Germany, Japan, 3items
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Citation | Journal: IUCrJ / Year: 2019 Title: Cryo-EM reveals the asymmetric assembly of squid hemocyanin. Authors: Yoshikazu Tanaka / Sanae Kato / Markus Stabrin / Stefan Raunser / Takashi Matsui / Christos Gatsogiannis / Abstract: The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. ...The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. Typically, the first six domains of each subunit assemble together to form the cylinder wall, while the C-terminal domains form a collar that fills or caps the cylinder. During evolution, various molluscs have been able to fine-tune their oxygen binding by deleting or adding C-terminal domains and adjusting their inner-collar architecture. However, squids have duplicated one of the wall domains of their subunits instead. Here, using cryo-EM and an optimized refinement protocol implemented in , this work tackled the symmetry-mismatched structure of squid hemocyanin, revealing the precise effect of this duplication on its quaternary structure and providing a potential model for its structural evolution. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6r83.cif.gz | 4.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6r83.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6r83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r83_validation.pdf.gz | 377.2 KB | Display | wwPDB validaton report |
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Full document | 6r83_full_validation.pdf.gz | 388.2 KB | Display | |
Data in XML | 6r83_validation.xml.gz | 406.7 KB | Display | |
Data in CIF | 6r83_validation.cif.gz | 682.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/6r83 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/6r83 | HTTPS FTP |
-Related structure data
Related structure data | 4750MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 379741.188 Da / Num. of mol.: 10 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) References: UniProt: A0A0P0UX03 |
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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 |
-Sample preparation
Component | Name: Squid Hemocyanin / Type: COMPLEX Details: TpH is a decamer of a 400 kDa subunit. Each subunit is composed by 8 paralogous O2 binding functional units (A,B,C,D,D*,E,F,G). The ten subunits of TpH acquire 4 different overall conformations. Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 3.8 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Todarodes pacificus (Japanese flying squid) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Cs: 0 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 56 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5092 |
EM imaging optics | Spherical aberration corrector: Microscope equipped with Cs corrector |
Image scans | Movie frames/image: 24 / Used frames/image: 1-24 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 359250 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196315 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |