Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 18071.57 
• Atom Count: 1272 
• Residue Count: 153 
• Unique protein chains: 1

3E55

Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser off

• DOI: 10.2210/pdb3E55/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Physeter macrocephalus


• Deposited: 2008-08-13 Released: 2009-02-24 
• Deposition Author(s): Tomita, A., Sato, T., Ichiyanagi, K., Nozawa, S., Ichikawa, H., Chollet, M., Kawai, F., Park, S.-Y., Koshihara, S., Adachi, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.205 
• R-Value Work: 0.153 

Literature

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.Y., Adachi, S.

(2009) Proc.Natl.Acad.Sci.USA 106: 2612-2616

• PubMed: 19204297 
• DOI: 10.1073/pnas.0807774106
• Primary Citation of Related Structures:  
  3EDB, 3EDA, 3ED9, 3ECZ, 3ECX, 3ECL, 3E5O, 3E5I, 3E4N, 2ZT4, 2ZT3, 2ZT2, 2ZT1, 2ZT0, 2ZSZ, 2ZSY, 2ZSX, 2ZST, 2ZSS, 2ZSR, 2ZSQ, 2ZSP, 2ZSO, 2ZSN


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 0  Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus) Go to Gene View: MB Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.205 
• R-Value Work: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 34.319	α = 90.00
b = 30.604	β = 105.39
c = 63.618	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-13 
• Released Date: 2009-02-24 
• Deposition Author(s): Tomita, A., Sato, T., Ichiyanagi, K., Nozawa, S., Ichikawa, H., Chollet, M., Kawai, F., Park, S.-Y., Koshihara, S., Adachi, S.

Revision History 

• Version 1.0: 2009-02-24
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-10-25
  Type: Refinement description