|Entry||Database: PDB / ID: 6r83|
|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||Tyrosinase copper-binding domain / Uncharacterised domain, di-copper centre / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Common central domain of tyrosinase / Haemocyanin beta-sandwich / oxidoreductase activity / metal ion binding / Hemocyanin subunit 1|
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 |
|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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
1a: Hemocyanin subunit 1
2a: Hemocyanin subunit 1
3a: Hemocyanin subunit 1
4a: Hemocyanin subunit 1
5a: Hemocyanin subunit 1
6a: Hemocyanin subunit 1
7a: Hemocyanin subunit 1
8a: Hemocyanin subunit 1
9a: Hemocyanin subunit 1
10a: Hemocyanin subunit 1
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
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|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: 1 / Source: NATURAL
|Molecular weight||Value: 3.8 MDa / Experimental value: NO|
|Source (natural)||Organism: Todarodes pacificus (Japanese flying squid)|
|Buffer solution||pH: 7.5|
|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
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Cs: 0 mm|
|Specimen holder||Cryogen: NITROGEN / 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|
|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|
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