› 5vmm

X-ray diffraction
3.6Å resolution

Staphylococcus aureus IsdB bound to human hemoglobin

Released:
DOI: 10.2210/pdb5vmm/pdb
PDB entry 5vmm coloured by chain, front view.
PDB entry 5vmm coloured by chain, side view.
PDB entry 5vmm coloured by chain, top view.
Source organisms:
Primary publication:
Structure-function analyses reveal key features in Staphylococcus aureus IsdB-associated unfolding of the heme-binding pocket of human hemoglobin.
Bowden CFM, Chan ACK, Li EJW, Arrieta AL, Eltis LD, Murphy MEP
J Biol Chem 293 177-190 (2018)
PMID: 29109153

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159521 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Hemoglobin subunit alpha Chains: A, C
Molecule details ›
Chains: A, C
Length: 141 amino acids
Theoretical weight: 15.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P69905 (Residues: 2-142; Coverage: 99%)
Gene names: HBA1, HBA2
Sequence domains: Globin
Structure domains: Globins
Hemoglobin subunit beta Chains: B, D
Molecule details ›
Chains: B, D
Length: 146 amino acids
Theoretical weight: 15.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P68871 (Residues: 2-147; Coverage: 99%)
Gene name: HBB
Sequence domains: Globin
Structure domains: Globins
Iron-regulated surface determinant protein B Chains: E, F
Molecule details ›
Chains: E, F
Length: 336 amino acids
Theoretical weight: 39.3 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7A656 (Residues: 126-459; Coverage: 55%)
Gene names: SA0976, frpB, isdB, sasJ, sirH
Sequence domains:
Iron-regulated surface determinant protein B Chains: H, J
Molecule details ›
Chains: H, J
Length: 142 amino acids
Theoretical weight: 16.44 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7A656 (Residues: 126-265; Coverage: 23%)
Gene names: SA0976, frpB, isdB, sasJ, sirH
Sequence domains: Iron Transport-associated domain
Structure domains: Immunoglobulin-like

Ligands and Environments

1 bound ligand:
Ligand HEM 2 x HEM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P21212
Unit cell:
a: 140.815Å b: 209.114Å c: 70.431Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.256 0.252 0.302
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Immunoglobulin germline gene variation and its impact on human disease.
Mikocziova et al. (2021)
5 more

11 mentions without citation

Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development.
Marchetti et al. (2020)
10 more