7DDR

Ancestral myoglobin aMbSp of Puijila Darwini relative (imidazol ligand)

• PDB DOI: https://doi.org/10.2210/pdb7DDR/pdb

• Classification: OXYGEN STORAGE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-10-29 Released: 2021-09-08 
• Deposition Author(s): Isogai, Y., Imamura, H., Nakae, S., Sumi, T., Takahashi, K., Shirai, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.202 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals.

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

(2021) iScience 24: 102920-102920

• PubMed: 34430810 
• DOI: https://doi.org/10.1016/j.isci.2021.102920
• Primary Citation of Related Structures:  
  7DDR, 7DDS, 7DDT, 7DDU


• PubMed Abstract: 
  

  Myoglobin (Mb) is highly concentrated in the myocytes of diving mammals such as whales and seals, in comparison with land animals, and its molecular evolution has played a crucial role in their deep-sea adaptation. We previously resurrected ancestral whale Mbs and demonstrated the evolutional strategies for higher solubility under macromolecular crowding conditions. Pinnipeds, such as seals and sea lions, are also expert diving mammals with Mb-rich muscles. In the present study, we resurrected ancestral pinniped Mbs and investigated their biochemical and structural properties. Comparisons between pinniped and whale Mbs revealed the common and distinctive strategies for the deep-sea adaptation. The overall evolution processes, gaining precipitant tolerance and improving thermodynamic stability, were commonly observed. However, the strategies for improving the folding stability differed, and the pinniped Mbs exploited the shielding of hydrophobic surfaces more effectively than the whale Mbs.

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Organizational Affiliation: 

Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan.

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: SAXS

Macromolecule Content

• Total Structure Weight: 17.84 kDa 
• Atom Count: 1,419 
• Modelled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral myoglobin aMbSp	A	154	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
IMD (Subject of Investigation/LOI)	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.202 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.02	α = 90
b = 62.72	β = 90
c = 65.52	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Isogai, Y., Imamura, H., Nakae, S., Sumi, T., Takahashi, K., Shirai, T.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	17H01818
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101111j0004

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description