Carbonmonoxy Sperm Whale Myoglobin at 140 K: Laser on [750 min]

Experimental Data Snapshot

  • Resolution: 1.21 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

Starting Model: experimental
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Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin.

Tomita, A.Sato, T.Ichiyanagi, K.Nozawa, S.Ichikawa, H.Chollet, M.Kawai, F.Park, S.-Y.Tsuduki, T.Yamato, T.Koshihara, S.Adachi, S.

(2009) Proc Natl Acad Sci U S A 106: 2612-2616

  • DOI: https://doi.org/10.1073/pnas.0807774106
  • Primary Citation of Related Structures:  
    2ZSN, 2ZSO, 2ZSP, 2ZSQ, 2ZSR, 2ZSS, 2ZST, 2ZSX, 2ZSY, 2ZSZ, 2ZT0, 2ZT1, 2ZT2, 2ZT3, 2ZT4, 3E4N, 3E55, 3E5I, 3E5O, 3ECL, 3ECX, 3ECZ, 3ED9, 3EDA, 3EDB

  • PubMed Abstract: 

    Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.

  • Organizational Affiliation

    Department of Materials Science, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin153Physeter catodonMutation(s): 0 
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: 1.21 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.381α = 90
b = 30.549β = 105.63
c = 63.841γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description