9BCH | pdb_00009bch

Solution structure of the hemoglobin receptor HbpA from Corynebacterium diphtheriae


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 21.92 kDa 
  • Atom Count: 1,544 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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

Revision History  (Full details and data files)

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