› 3wct

X-ray diffraction
2.4Å resolution

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form

Released:
DOI: 10.2210/pdb3wct/pdb
Model geometry
Fit model/data
PDB entry 3wct coloured by chain, front view.
PDB entry 3wct coloured by chain, side view.
PDB entry 3wct coloured by chain, top view.
Source organism: Lamellibrachia satsuma
Primary publication:
The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins.
Numoto N, Nakagawa T, Ohara R, Hasegawa T, Kita A, Yoshida T, Maruyama T, Imai K, Fukumori Y, Miki K
Acta Crystallogr D Biol Crystallogr 70 1823-31 (2014)
PMID: 25004960

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-197402 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Extracellular globin Chains: A, E
Molecule details ›
Chains: A, E
Length: 146 amino acids
Theoretical weight: 16.37 KDa
Source organism: Lamellibrachia satsuma
UniProt:
  • Canonical: S0BBU7 (Residues: 20-165; Coverage: 100%)
Gene name: v2hb-A1
Sequence domains: Globin
Structure domains: Globins
Extracellular globin Chains: B, F
Molecule details ›
Chains: B, F
Length: 144 amino acids
Theoretical weight: 15.95 KDa
Source organism: Lamellibrachia satsuma
UniProt:
  • Canonical: S0BBR6 (Residues: 17-160; Coverage: 100%)
Gene names: ghbA2, v2hb-A2
Sequence domains: Globin
Structure domains: Globins
Extracellular globin Chains: C, G
Extracellular globin Chains: D, H

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN, FUC
Carbohydrate polymer
3 bound ligands:
Ligand HEM 8 x HEM
Ligand OXY 8 x OXY
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P63
Unit cell:
a: 108.556Å b: 108.556Å c: 193.552Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.216 0.216 0.264

Quick links

Citations

1 citations in other articles

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)

1 mention without citation

Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Numoto et al. (2022)