9SZW | pdb_00009szw

Human carboxyhemoglobin bound to full-length Staphylococcus aureus IsdH - IsdH:Hbdim complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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

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This is version 1.1 of the entry. See complete history

Literature

Refining the mechanism of heme acquisition from free hemoglobin by Staphylococcus aureus IsdH.

Comani, V.B.De Bei, O.Paris, G.Marchetti, M.Pancrazi, F.Campanini, B.Ronda, L.Luisi, B.F.Faggiano, S.Bizzarri, A.R.Bettati, S.

(2026) Proc Natl Acad Sci U S A 123

  • DOI: https://doi.org/10.1073/pnas.2601134123
  • Primary Citation Related Structures: 
    9SZW

  • PubMed Abstract: 

    Staphylococcus aureus is a human pathogen whose virulence depends on iron acquisition. The bacterium expresses the hemophores IsdB and IsdH that enable heme capture from host hemoglobin (Hb). Unlike IsdB, IsdH can bind both free Hb and Hb:haptoglobin (Hb:Hp) complexes. Here, we present a comprehensive structural analysis of full-length IsdH in complex with free Hb, overcoming the limitations of previous studies based on truncated IsdH constructs. Cryo-EM revealed a previously unobserved oligomeric state and a unique binding pose of the N-terminal Hb-binding domain, likely representing the initial step of Hb engagement. Time-resolved and single-molecule force spectroscopy experiments delineated the sequential steps and mechanical aspects of Hb binding and heme extraction. Together, these findings provide an integrated structural and functional view of the IsdH-Hb interaction in the absence of Hp, as may occur during hemolysis, and offer insights into S. aureus heme scavenging and potential avenues for therapeutic inhibition.


  • Organizational Affiliation
    • Department of Food and Drug, University of Parma, Parma 43124, Italy.

Macromolecule Content 

  • Total Structure Weight: 102.43 kDa 
  • Atom Count: 6,134 
  • Modeled Residue Count: 757 
  • Deposited Residue Count: 901 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha140Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta145Homo 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein H616Staphylococcus aureusMutation(s): 0 
Gene Names: isdHharAsasIMW1674
UniProt
Find proteins for Q8NW39 (Staphylococcus aureus (strain MW2))
Explore Q8NW39 
Go to UniProtKB:  Q8NW39
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NW39
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0
MODEL REFINEMENTISOLDE

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly2020AE3LTA
Wellcome TrustUnited Kingdom200873/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Data collection, Database references