› 1yhu

X-ray diffraction
3.15Å resolution

Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.

Released:
DOI: 10.2210/pdb1yhu/pdb
PDB entry 1yhu coloured by chain, front view.
PDB entry 1yhu coloured by chain, side view.
PDB entry 1yhu coloured by chain, top view.
Source organism: Riftia pachyptila
Primary publication:
Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.
Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE
Proc Natl Acad Sci U S A 102 2713-8 (2005)
PMID: 15710902

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-160433 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Globin domain-containing protein Chains: A, E, I, M, Q, U
Molecule details ›
Chains: A, E, I, M, Q, U
Length: 145 amino acids
Theoretical weight: 15.8 KDa
Source organism: Riftia pachyptila
UniProt:
  • Canonical: Q8IFK4 (Residues: 1-115; Coverage: 100%)
Gene name: hbA1
Sequence domains: Globin
Structure domains: Globins
Giant hemoglobins B chain Chains: B, F, J, N, R, V
Molecule details ›
Chains: B, F, J, N, R, V
Length: 144 amino acids
Theoretical weight: 16.16 KDa
Source organism: Riftia pachyptila
UniProt:
  • Canonical: P80592 (Residues: 1-144; Coverage: 100%)
Sequence domains: Globin
Structure domains: Globins
Globin domain-containing protein Chains: C, G, K, O, S, W
Molecule details ›
Chains: C, G, K, O, S, W
Length: 148 amino acids
Theoretical weight: 15.29 KDa
Source organism: Riftia pachyptila
UniProt:
  • Canonical: Q8IFK2 (Residues: 1-118; Coverage: 100%)
Gene name: hbB1a
Sequence domains: Globin
Structure domains: Globins
Globin domain-containing protein Chains: D, H, L, P, T, X
Molecule details ›
Chains: D, H, L, P, T, X
Length: 149 amino acids
Theoretical weight: 16.16 KDa
Source organism: Riftia pachyptila
UniProt:
  • Canonical: Q8IFJ9 (Residues: 1-117; Coverage: 100%)
Gene name: hbB2
Sequence domains: Globin
Structure domains: Globins

Ligands and Environments

3 bound ligands:
Ligand HEM 24 x HEM
Ligand OXY 24 x OXY
Ligand ZN 12 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P41212
Unit cell:
a: 195.84Å b: 195.84Å c: 308.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.243 0.271

Quick links

Citations

8 review citations

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis.
Dubilier et al. (2008)
7 more

4 mentions without citation

Hydrogen sulfide and hemeproteins: knowledge and mysteries.
Pietri et al. (2011)
3 more