5YCH | pdb_00005ych

Ancestral myoglobin aMbWb of Basilosaurus relative (monophyly)

• PDB DOI: https://doi.org/10.2210/pdb5YCH/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-07 Released: 2018-09-19 
• Deposition Author(s): Isogai, Y., Imamura, H., Nakae, S., Sumi, T., Takahashi, K., Nakagawa, T., Tsuneshige, A., Shirai, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Agency for Medical Research and Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.207 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 30442991 
• DOI: https://doi.org/10.1038/s41598-018-34984-6
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan. [e-mail].
Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan.
Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan.
Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan.
Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 18.05 kDa 
• Atom Count: 1,458 
• Modeled Residue Count: 153 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral myoglobin aMbWb of Basilosaurus relative (monophyly)	A	154	Physeter macrocephalus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.207 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.37	α = 90
b = 30.43	β = 105.81
c = 63.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Isogai, Y., Imamura, H., Nakae, S., Sumi, T., Takahashi, K., Nakagawa, T., Tsuneshige, A., Shirai, T.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP17H01818
Japan Agency for Medical Research and Development	Japan	17am0101069j0001

Revision History  

• 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