› 2zfo

X-ray diffraction
1.95Å resolution

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

Released:
DOI: 10.2210/pdb2zfo/pdb
PDB entry 2zfo coloured by chain, front view.
PDB entry 2zfo coloured by chain, side view.
PDB entry 2zfo coloured by chain, top view.
Source organism: Oligobrachia mashikoi
Primary publication:
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
Proteins 73 113-25 (2008)
PMID: 18398907

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177350 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Extracellular giant hemoglobin major globin subunit A1 Chain: A
Molecule details ›
Chain: A
Length: 140 amino acids
Theoretical weight: 15.19 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q7M419 (Residues: 17-156; Coverage: 100%)
Gene name: ghbA1
Sequence domains: Globin
Structure domains: Globins
Extracellular giant hemoglobin major globin subunit A2 Chain: B
Molecule details ›
Chain: B
Length: 142 amino acids
Theoretical weight: 15.33 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q7M413 (Residues: 17-158; Coverage: 100%)
Gene name: ghbA2
Sequence domains: Globin
Structure domains: Globins
Extracellular giant hemoglobin major globin subunit B2 Chain: C
Molecule details ›
Chain: C
Length: 147 amino acids
Theoretical weight: 15.62 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q7M418 (Residues: 17-163; Coverage: 100%)
Gene name: ghbB2
Sequence domains: Globin
Structure domains: Globins
Extracellular giant hemoglobin major globin subunit B1 Chain: D
Molecule details ›
Chain: D
Length: 145 amino acids
Theoretical weight: 14.69 KDa
Source organism: Oligobrachia mashikoi
UniProt:
  • Canonical: Q5KSB7 (Residues: 17-161; Coverage: 100%)
Gene name: ghbB1
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

3 bound ligands:
Ligand HEM 4 x HEM
Ligand OXY 1 x OXY
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: R32
Unit cell:
a: 110.96Å b: 110.96Å c: 271.58Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.169 0.169 0.202

Quick links

Citations

1 review citation

Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins.
Ronda et al. (2013)
3 other articles

1 mention without citation

Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Numoto et al. (2021)