6R83

CryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH)

• PDB DOI: https://doi.org/10.2210/pdb6R83/pdb
• EM Map EMD-4750: EMDB EMDataResource

• Classification: OXYGEN TRANSPORT
• Organism(s): Todarodes pacificus
• Mutation(s): No 


• Deposited: 2019-03-31 Released: 2019-05-08 
• Deposition Author(s): Tanaka, Y., Kato, S., Stabrin, M., Raunser, S., Matsui, T., Gatsogiannis, C.
• Funding Organization(s): Max Planck Society, German Research Foundation, Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM reveals the asymmetric assembly of squid hemocyanin.

Tanaka, Y., Kato, S., Stabrin, M., Raunser, S., Matsui, T., Gatsogiannis, C.

(2019) IUCrJ 6: 426-437

• PubMed: 31098023 
• DOI: https://doi.org/10.1107/S205225251900321X
• Primary Citation of Related Structures:  
  6R83


• PubMed 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. 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 SPHIRE , 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.

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Organizational Affiliation: 

Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 10-mer - A10 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 3,797.41 kDa 
• Atom Count: 161,300 
• Modelled Residue Count: 32,620 
• Deposited Residue Count: 33,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemocyanin subunit 1	A [auth 1a], B [auth 2a], C [auth 3a], D [auth 4a], E [auth 5a], F [auth 6a], G [auth 7a], H [auth 8a], I [auth 9a], J [auth 10a]	3,314	Todarodes pacificus	Mutation(s): 0
UniProt
Find proteins for A0A0P0UX03 (Todarodes pacificus) Explore A0A0P0UX03  Go to UniProtKB:  A0A0P0UX03

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPHIRE

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): Tanaka, Y., Kato, S., Stabrin, M., Raunser, S., Matsui, T., Gatsogiannis, C.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
German Research Foundation	Germany	FOR1905
Japan Society for the Promotion of Science	Japan	26291008;24000011;15KK0248;16H00748;17K07942

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Refinement description