9O0J | pdb_00009o0j

HtaA CR1 domain from Corynebacterium diphtheriae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.248 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural basis of heme scavenging by the ChtA and HtaA hemophores in Corynebacterium diphtheriae.

Ford, J.Goring, A.K.Lee, Y.Chen, M.Mahoney, B.J.Sawaya, M.R.Shafaat, H.S.Loo, J.A.Clubb, R.T.

(2025) J Biological Chem 301: 110633-110633

  • DOI: https://doi.org/10.1016/j.jbc.2025.110633
  • Primary Citation Related Structures: 
    9O0J, 9O0K

  • PubMed Abstract: 

    Corynebacterium diphtheriae causes diphtheria, a potentially fatal infectious disease that damages tissues in the upper respiratory tract. In order to proliferate, this pathogen acquires the essential nutrient iron from heme (iron-protoporphyrin IX) primarily found in human hemoglobin (Hb). C. diphtheriae secretes ChtA and HtaA hemophore proteins that bind ferric heme (hemin) via Conserved Region (CR) domains. Here we demonstrate that their CR domains scavenge hemin after it is spontaneously released from Hb, and define the structural basis of hemin binding to ChtA and the N-terminal CR domain from HtaA by determining X-ray crystal structures of their protein-hemin complexes. Resonance Raman and EPR experiments demonstrate that the CR domains from ChtA and HtaA engage in pentacoordinate hemin binding through a conserved iron-tyrosyl linkage, though variations in their hemin pockets alter the way they stabilize the axial tyrosine and mask hemin's metal. The importance of these interactions is probed using isothermal titration calorimetry experiments, which represent the first quantitative assessment of CR-hemin affinity and reveal that ChtA binds hemin via an enthalpically driven process. Hemin partitioning experiments using native mass spectrometry demonstrate that the cohort of CR domains within C. diphtheriae's hemin-uptake system have dissociation constants for hemin between 0.8 to 22 nM, raising the possibility that affinity differences contribute to the directional flow of hemin into the cell. Collectively, the results of this work provide insight into how C. diphtheriae and other pathogenic and commensal corynebacterium species utilize CR domains to scavenge iron rich hemin from their environment.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA.

Macromolecule Content 

  • Total Structure Weight: 194.02 kDa 
  • Atom Count: 14,103 
  • Modeled Residue Count: 1,780 
  • Deposited Residue Count: 1,780 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane protein HtaACR1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
178Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP0625
UniProt
Find proteins for Q6NIZ1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NIZ1 
Go to UniProtKB:  Q6NIZ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NIZ1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
BA [auth J]
K [auth A]
N [auth B]
O [auth C]
P [auth D]
BA [auth J],
K [auth A],
N [auth B],
O [auth C],
P [auth D],
R [auth E],
S [auth F],
V [auth G],
X [auth H],
Y [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PEG

Query on PEG



Download:Ideal Coordinates CCD File
L [auth A],
T [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CA [auth J],
W [auth G],
Z [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth I],
M [auth A],
Q [auth D],
U [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.703α = 90
b = 209.062β = 90.028
c = 153.846γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
STARANISOdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI161828-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references
  • Version 1.2: 2025-09-17
    Changes: Refinement description
  • Version 1.3: 2025-10-08
    Changes: Database references