9BCJ

Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Literature

Molecular basis of hemoglobin binding and heme removal in Corynebacterium diphtheriae.

Mahoney, B.J.Lyman, L.R.Ford, J.Soule, J.Cheung, N.A.Goring, A.K.Ellis-Guardiola, K.Collazo, M.J.Cascio, D.Ton-That, H.Schmitt, M.P.Clubb, R.T.

(2025) Proc Natl Acad Sci U S A 122: e2411833122-e2411833122

  • DOI: https://doi.org/10.1073/pnas.2411833122
  • Primary Citation of Related Structures:  
    9BCH, 9BCJ

  • PubMed Abstract: 

    To successfully mount infections, nearly all bacterial pathogens must acquire iron, a key metal cofactor that primarily resides within human hemoglobin. Corynebacterium diphtheriae causes the life-threatening respiratory disease diphtheria and captures hemoglobin for iron scavenging using the surface-displayed receptor HbpA. Here, we show using X-ray crystallography, NMR, and in situ binding measurements that C. diphtheriae selectively captures iron-loaded hemoglobin by partially ensconcing the heme molecules of its α subunits. Quantitative growth and heme release measurements are compatible with C. diphtheriae acquiring heme passively released from hemoglobin's β subunits. We propose a model in which HbpA and heme-binding receptors collectively function on the C. diphtheriae surface to capture hemoglobin and its spontaneously released heme. Acquisition mechanisms that exploit the propensity of hemoglobin's β subunit to release heme likely represent a common strategy used by bacterial pathogens to obtain iron during infections.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein198Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP2330
UniProt
Find proteins for Q6NEE5 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NEE5 
Go to UniProtKB:  Q6NEE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NEE5
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.925α = 90
b = 58.925β = 90
c = 286.146γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
BUCCANEERmodel building
Cootmodel building
BUSTERrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI161828
Department of Energy (DOE, United States)United StatesDE-FC02-02ER63421

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release