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Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins

Numoto, N.Nakagawa, T.Kita, A.Sasayama, Y.Fukumori, Y.Miki, K.

(2008) Proteins 73: 113-125

  • DOI: 10.1002/prot.22040

  • PubMed Abstract: 
  • Recent crystallographic studies have revealed the structures of some invertebrate extracellular giant hemoglobins of 3,600 kDa or 400 kDa and their common quaternary structure of dodecameric subassembly composed of four kinds of globin subunits (A1, ...

    Recent crystallographic studies have revealed the structures of some invertebrate extracellular giant hemoglobins of 3,600 kDa or 400 kDa and their common quaternary structure of dodecameric subassembly composed of four kinds of globin subunits (A1, A2, B1, and B2). These results have provided insight into the mechanisms of their unique functional properties of oxygen binding and sulfide binding. All of these structures were solved with oxygenated or CO-liganded forms at low or moderate resolutions. We have determined the crystal structure of 400 kDa Hb from a polychaete Oligobrachia mashikoi at 1.95 A resolution. The electron densities at higher resolution confirm the existence of an isoform of the B1 subunit because of the inconsistency with the model that was built from the formerly known amino acid sequence. The brownish color of the crystals used in this study and the absorption spectrum from the dissolved crystals strongly indicated that the obtained structure was a ferric met state, whereas complete absence of electron density around the distal heme pockets were observed at the A2, B1, and B2 subunits. We concluded that the obtained structure was in unliganded met forms at three of four globin subunits in the 24mer assembly and in oxygenated forms at the remaining A1 subunits. The partially unliganded structure showed remarkable structural changes at the AB loop regions causing quaternary rearrangements of the EF-dimer structure. In contrast, few changes occurred at the interface regions composed of the E and F helices. These results suggest that the ligand-induced structural changes of Oligobrachia Hb are quite different from those of the well-studied mollusk Hb having the same EF-dimer structure. The structural rearrangements make the dodecameric subassembly form a tighter conformation than those of fully oxygenated or CO-liganded dodecamer structure.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit A1
A
140Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbA1
Find proteins for Q7M419 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M419
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit A2
B
142Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbA2
Find proteins for Q7M413 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M413
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit B2
C
147Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbB2
Find proteins for Q7M418 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M418
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit B1
D
145Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbB1
Find proteins for Q5KSB7 (Oligobrachia mashikoi)
Go to UniProtKB:  Q5KSB7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 110.960α = 90.00
b = 110.960β = 90.00
c = 271.580γ = 120.00
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance