Sperm whale myoglobin swMb

Experimental Data Snapshot

  • Resolution: 0.77 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

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This is version 1.2 of the entry. See complete history


Tracing whale myoglobin evolution by resurrecting ancient proteins.

Isogai, Y.Imamura, H.Nakae, S.Sumi, T.Takahashi, K.I.Nakagawa, T.Tsuneshige, A.Shirai, T.

(2018) Sci Rep 8: 16883-16883

  • DOI: https://doi.org/10.1038/s41598-018-34984-6
  • Primary Citation of Related Structures:  
    5YCE, 5YCG, 5YCH, 5YCI, 5YCJ

  • PubMed Abstract: 

    Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.

  • Organizational Affiliation

    Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan. yisogai@pu-toyama.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Physeter catodonMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.77 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.18α = 90
b = 30.66β = 105.49
c = 63.57γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP17H01818
Japan Agency for Medical Research and DevelopmentJapan17am0101069j0001

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description